diff --git a/cmd/link.go b/cmd/link.go
index 59c93545c..65b8b5f08 100644
--- a/cmd/link.go
+++ b/cmd/link.go
@@ -8,7 +8,6 @@ import (
 	"github.com/spf13/cobra"
 	"github.com/spf13/viper"
 	"github.com/supabase/cli/internal/link"
-	"github.com/supabase/cli/internal/utils"
 	"github.com/supabase/cli/internal/utils/flags"
 	"golang.org/x/term"
 )
@@ -31,8 +30,7 @@ var (
 				return err
 			}
 			fsys := afero.NewOsFs()
-			utils.Config.ProjectId = flags.ProjectRef
-			if err := utils.LoadConfigFS(fsys); err != nil {
+			if err := flags.LoadConfig(fsys); err != nil {
 				return err
 			}
 			return link.Run(ctx, flags.ProjectRef, fsys)
diff --git a/internal/bootstrap/bootstrap.go b/internal/bootstrap/bootstrap.go
index 677ef1530..8310a82fb 100644
--- a/internal/bootstrap/bootstrap.go
+++ b/internal/bootstrap/bootstrap.go
@@ -95,7 +95,7 @@ func Run(ctx context.Context, starter StarterTemplate, fsys afero.Fs, options ..
 		return err
 	}
 	// 4. Link project
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	link.LinkServices(ctx, flags.ProjectRef, tenant.NewApiKey(keys).Anon, fsys)
diff --git a/internal/config/push/push.go b/internal/config/push/push.go
index b1b887765..d2dadddc3 100644
--- a/internal/config/push/push.go
+++ b/internal/config/push/push.go
@@ -7,16 +7,20 @@ import (
 
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/config"
 )
 
 func Run(ctx context.Context, ref string, fsys afero.Fs) error {
-	utils.Config.ProjectId = ref
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	client := config.NewConfigUpdater(*utils.GetSupabase())
-	remote, _ := utils.Config.GetRemoteByProjectRef(ref)
+	remote, err := utils.Config.GetRemoteByProjectRef(ref)
+	if err != nil {
+		// Use base config when no remote is declared
+		remote.ProjectId = ref
+	}
 	fmt.Fprintln(os.Stderr, "Pushing config to project:", remote.ProjectId)
 	console := utils.NewConsole()
 	keep := func(name string) bool {
diff --git a/internal/db/branch/create/create.go b/internal/db/branch/create/create.go
index 085e10f9d..550128376 100644
--- a/internal/db/branch/create/create.go
+++ b/internal/db/branch/create/create.go
@@ -14,6 +14,7 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 var (
@@ -22,7 +23,7 @@ var (
 )
 
 func Run(branch string, fsys afero.Fs) error {
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if err := utils.AssertSupabaseDbIsRunning(); err != nil {
diff --git a/internal/db/branch/delete/delete.go b/internal/db/branch/delete/delete.go
index f59f5e51c..ea14cd34d 100644
--- a/internal/db/branch/delete/delete.go
+++ b/internal/db/branch/delete/delete.go
@@ -12,10 +12,11 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 func Run(branch string, fsys afero.Fs) error {
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if err := utils.AssertSupabaseDbIsRunning(); err != nil {
diff --git a/internal/db/branch/switch_/switch_.go b/internal/db/branch/switch_/switch_.go
index 462b26c69..d11803e88 100644
--- a/internal/db/branch/switch_/switch_.go
+++ b/internal/db/branch/switch_/switch_.go
@@ -12,12 +12,13 @@ import (
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/db/reset"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 func Run(ctx context.Context, target string, fsys afero.Fs, options ...func(*pgx.ConnConfig)) error {
 	// 1. Sanity checks
 	{
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := flags.LoadConfig(fsys); err != nil {
 			return err
 		}
 		if err := utils.AssertSupabaseDbIsRunning(); err != nil {
diff --git a/internal/db/diff/diff.go b/internal/db/diff/diff.go
index 6c5faa892..d54f5e534 100644
--- a/internal/db/diff/diff.go
+++ b/internal/db/diff/diff.go
@@ -24,6 +24,7 @@ import (
 	"github.com/supabase/cli/internal/db/start"
 	"github.com/supabase/cli/internal/gen/keys"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 	"github.com/supabase/cli/pkg/parser"
 )
@@ -32,7 +33,7 @@ type DiffFunc func(context.Context, string, string, []string) (string, error)
 
 func Run(ctx context.Context, schema []string, file string, config pgconn.Config, differ DiffFunc, fsys afero.Fs, options ...func(*pgx.ConnConfig)) (err error) {
 	// Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if utils.IsLocalDatabase(config) {
diff --git a/internal/db/diff/pgadmin.go b/internal/db/diff/pgadmin.go
index 298023580..55046bf24 100644
--- a/internal/db/diff/pgadmin.go
+++ b/internal/db/diff/pgadmin.go
@@ -11,6 +11,7 @@ import (
 	"github.com/supabase/cli/internal/db/start"
 	"github.com/supabase/cli/internal/migration/new"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/config"
 )
 
@@ -35,7 +36,7 @@ func SaveDiff(out, file string, fsys afero.Fs) error {
 func RunPgAdmin(ctx context.Context, schema []string, file string, config pgconn.Config, fsys afero.Fs) error {
 	// Sanity checks.
 	{
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := flags.LoadConfig(fsys); err != nil {
 			return err
 		}
 		if err := utils.AssertSupabaseDbIsRunning(); err != nil {
diff --git a/internal/db/pull/pull.go b/internal/db/pull/pull.go
index f6a235e11..6cc8dccab 100644
--- a/internal/db/pull/pull.go
+++ b/internal/db/pull/pull.go
@@ -18,6 +18,7 @@ import (
 	"github.com/supabase/cli/internal/migration/new"
 	"github.com/supabase/cli/internal/migration/repair"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
@@ -35,7 +36,7 @@ var (
 
 func Run(ctx context.Context, schema []string, config pgconn.Config, name string, fsys afero.Fs, options ...func(*pgx.ConnConfig)) error {
 	// 1. Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	// 2. Check postgres connection
diff --git a/internal/db/push/push.go b/internal/db/push/push.go
index 2141255ae..7e5241558 100644
--- a/internal/db/push/push.go
+++ b/internal/db/push/push.go
@@ -31,9 +31,10 @@ func Run(ctx context.Context, dryRun, ignoreVersionMismatch bool, includeRoles,
 	}
 	var seeds []migration.SeedFile
 	if includeSeed {
-		if remote, _ := utils.Config.GetRemoteByProjectRef(flags.ProjectRef); !remote.Db.Seed.Enabled {
-			fmt.Fprintln(os.Stderr, "Skipping seed because it is disabled in config.toml for project:", remote.ProjectId)
-		} else if seeds, err = migration.GetPendingSeeds(ctx, remote.Db.Seed.SqlPaths, conn, afero.NewIOFS(fsys)); err != nil {
+		// TODO: flag should override config but we don't resolve glob paths when seed is disabled.
+		if !utils.Config.Db.Seed.Enabled {
+			fmt.Fprintln(os.Stderr, "Skipping seed because it is disabled in config.toml for project:", flags.ProjectRef)
+		} else if seeds, err = migration.GetPendingSeeds(ctx, utils.Config.Db.Seed.SqlPaths, conn, afero.NewIOFS(fsys)); err != nil {
 			return err
 		}
 	}
diff --git a/internal/db/remote/changes/changes.go b/internal/db/remote/changes/changes.go
index c735b5984..9aa4a47b0 100644
--- a/internal/db/remote/changes/changes.go
+++ b/internal/db/remote/changes/changes.go
@@ -8,6 +8,7 @@ import (
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/db/diff"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
@@ -15,7 +16,7 @@ var output string
 
 func Run(ctx context.Context, schema []string, config pgconn.Config, fsys afero.Fs) error {
 	// Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 
diff --git a/internal/db/remote/commit/commit.go b/internal/db/remote/commit/commit.go
index f9062d492..6e00a0295 100644
--- a/internal/db/remote/commit/commit.go
+++ b/internal/db/remote/commit/commit.go
@@ -15,12 +15,13 @@ import (
 	"github.com/supabase/cli/internal/migration/list"
 	"github.com/supabase/cli/internal/migration/repair"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
 func Run(ctx context.Context, schema []string, config pgconn.Config, fsys afero.Fs) error {
 	// Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 
diff --git a/internal/db/reset/reset.go b/internal/db/reset/reset.go
index 3830a019d..307f14f55 100644
--- a/internal/db/reset/reset.go
+++ b/internal/db/reset/reset.go
@@ -27,7 +27,6 @@ import (
 	"github.com/supabase/cli/internal/migration/repair"
 	"github.com/supabase/cli/internal/seed/buckets"
 	"github.com/supabase/cli/internal/utils"
-	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
@@ -250,15 +249,11 @@ func resetRemote(ctx context.Context, version string, config pgconn.Config, fsys
 	if err := migration.ApplyMigrations(ctx, migrations, conn, afero.NewIOFS(fsys)); err != nil {
 		return err
 	}
-	remote, _ := utils.Config.GetRemoteByProjectRef(flags.ProjectRef)
-	if !remote.Db.Seed.Enabled {
-		fmt.Fprintln(os.Stderr, "Skipping seed because it is disabled in config.toml for project:", remote.ProjectId)
-		return nil
-	} else if !utils.Config.Db.Seed.Enabled {
+	if !utils.Config.Db.Seed.Enabled {
 		// Skip because --no-seed flag is set
 		return nil
 	}
-	seeds, err := migration.GetPendingSeeds(ctx, remote.Db.Seed.SqlPaths, conn, afero.NewIOFS(fsys))
+	seeds, err := migration.GetPendingSeeds(ctx, utils.Config.Db.Seed.SqlPaths, conn, afero.NewIOFS(fsys))
 	if err != nil {
 		return err
 	}
diff --git a/internal/db/start/start.go b/internal/db/start/start.go
index aa8b9cee5..4180fe05c 100644
--- a/internal/db/start/start.go
+++ b/internal/db/start/start.go
@@ -23,6 +23,7 @@ import (
 	"github.com/supabase/cli/internal/migration/apply"
 	"github.com/supabase/cli/internal/status"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
@@ -39,7 +40,7 @@ var (
 )
 
 func Run(ctx context.Context, fromBackup string, fsys afero.Fs) error {
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if err := utils.AssertSupabaseDbIsRunning(); err == nil {
diff --git a/internal/functions/deploy/deploy.go b/internal/functions/deploy/deploy.go
index 5ee2ae845..5b6bb8e47 100644
--- a/internal/functions/deploy/deploy.go
+++ b/internal/functions/deploy/deploy.go
@@ -18,7 +18,7 @@ import (
 
 func Run(ctx context.Context, slugs []string, projectRef string, noVerifyJWT *bool, importMapPath string, fsys afero.Fs) error {
 	// Load function config and project id
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	} else if len(slugs) > 0 {
 		for _, s := range slugs {
@@ -60,8 +60,7 @@ func GetFunctionSlugs(fsys afero.Fs) (slugs []string, err error) {
 		}
 	}
 	// Add all function slugs declared in config file
-	remote, _ := utils.Config.GetRemoteByProjectRef(flags.ProjectRef)
-	for slug := range remote.Functions {
+	for slug := range utils.Config.Functions {
 		slugs = append(slugs, slug)
 	}
 	return slugs, nil
@@ -82,10 +81,9 @@ func GetFunctionConfig(slugs []string, importMapPath string, noVerifyJWT *bool,
 	if len(importMapPath) > 0 && !filepath.IsAbs(importMapPath) {
 		importMapPath = filepath.Join(utils.CurrentDirAbs, importMapPath)
 	}
-	remote, _ := utils.Config.GetRemoteByProjectRef(flags.ProjectRef)
 	functionConfig := make(config.FunctionConfig, len(slugs))
 	for _, name := range slugs {
-		function := remote.Functions[name]
+		function := utils.Config.Functions[name]
 		// Precedence order: flag > config > fallback
 		functionDir := filepath.Join(utils.FunctionsDir, name)
 		if len(function.Entrypoint) == 0 {
diff --git a/internal/functions/download/download.go b/internal/functions/download/download.go
index e3b68cae9..ca99c1bcf 100644
--- a/internal/functions/download/download.go
+++ b/internal/functions/download/download.go
@@ -16,6 +16,7 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/api"
 )
 
@@ -112,7 +113,7 @@ func Run(ctx context.Context, slug string, projectRef string, useLegacyBundle bo
 		return RunLegacy(ctx, slug, projectRef, fsys)
 	}
 	// 1. Sanity check
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	// 2. Download eszip to temp file
diff --git a/internal/functions/new/new.go b/internal/functions/new/new.go
index f787ce90c..5eca5b67a 100644
--- a/internal/functions/new/new.go
+++ b/internal/functions/new/new.go
@@ -11,6 +11,7 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 var (
@@ -45,7 +46,7 @@ func Run(ctx context.Context, slug string, fsys afero.Fs) error {
 		}
 
 		// Load config if available
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := flags.LoadConfig(fsys); err != nil {
 			utils.CmdSuggestion = ""
 		}
 
diff --git a/internal/functions/serve/serve.go b/internal/functions/serve/serve.go
index 62811d769..485d8c7cf 100644
--- a/internal/functions/serve/serve.go
+++ b/internal/functions/serve/serve.go
@@ -19,6 +19,7 @@ import (
 	"github.com/supabase/cli/internal/functions/deploy"
 	"github.com/supabase/cli/internal/secrets/set"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 type InspectMode string
@@ -70,7 +71,7 @@ var (
 
 func Run(ctx context.Context, envFilePath string, noVerifyJWT *bool, importMapPath string, runtimeOption RuntimeOption, fsys afero.Fs) error {
 	// 1. Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if err := utils.AssertSupabaseDbIsRunning(); err != nil {
diff --git a/internal/gen/types/types.go b/internal/gen/types/types.go
index b399cfb5c..9ffc7dc72 100644
--- a/internal/gen/types/types.go
+++ b/internal/gen/types/types.go
@@ -31,8 +31,7 @@ func Run(ctx context.Context, projectId string, dbConfig pgconn.Config, lang str
 	originalURL := utils.ToPostgresURL(dbConfig)
 	// Add default schemas if --schema flag is not specified
 	if len(schemas) == 0 {
-		remote, _ := utils.Config.GetRemoteByProjectRef(projectId)
-		schemas = utils.RemoveDuplicates(append([]string{"public"}, remote.Api.Schemas...))
+		schemas = utils.RemoveDuplicates(append([]string{"public"}, utils.Config.Api.Schemas...))
 	}
 	included := strings.Join(schemas, ",")
 
diff --git a/internal/migration/squash/squash.go b/internal/migration/squash/squash.go
index 2ed9e6252..4aad8b832 100644
--- a/internal/migration/squash/squash.go
+++ b/internal/migration/squash/squash.go
@@ -20,6 +20,7 @@ import (
 	"github.com/supabase/cli/internal/migration/list"
 	"github.com/supabase/cli/internal/migration/repair"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/migration"
 )
 
@@ -34,7 +35,7 @@ func Run(ctx context.Context, version string, config pgconn.Config, fsys afero.F
 			return err
 		}
 	}
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	// 1. Squash local migrations
diff --git a/internal/seed/buckets/buckets.go b/internal/seed/buckets/buckets.go
index b460fdc79..365c3a395 100644
--- a/internal/seed/buckets/buckets.go
+++ b/internal/seed/buckets/buckets.go
@@ -26,9 +26,8 @@ func Run(ctx context.Context, projectRef string, interactive bool, fsys afero.Fs
 		}
 		return shouldOverwrite
 	}
-	remote, _ := utils.Config.GetRemoteByProjectRef(projectRef)
-	if err := api.UpsertBuckets(ctx, remote.Storage.Buckets, filter); err != nil {
+	if err := api.UpsertBuckets(ctx, utils.Config.Storage.Buckets, filter); err != nil {
 		return err
 	}
-	return api.UpsertObjects(ctx, remote.Storage.Buckets, utils.NewRootFS(fsys))
+	return api.UpsertObjects(ctx, utils.Config.Storage.Buckets, utils.NewRootFS(fsys))
 }
diff --git a/internal/start/start.go b/internal/start/start.go
index 6f75d1377..2501d5b8d 100644
--- a/internal/start/start.go
+++ b/internal/start/start.go
@@ -37,7 +37,7 @@ import (
 func Run(ctx context.Context, fsys afero.Fs, excludedContainers []string, ignoreHealthCheck bool) error {
 	// Sanity checks.
 	{
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := flags.LoadConfig(fsys); err != nil {
 			return err
 		}
 		if err := utils.AssertSupabaseDbIsRunning(); err == nil {
diff --git a/internal/status/status.go b/internal/status/status.go
index 1b9d02f90..68eae2fe3 100644
--- a/internal/status/status.go
+++ b/internal/status/status.go
@@ -19,6 +19,7 @@ import (
 	"github.com/go-errors/errors"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 	"github.com/supabase/cli/pkg/fetcher"
 )
 
@@ -67,7 +68,7 @@ func (c *CustomName) toValues(exclude ...string) map[string]string {
 
 func Run(ctx context.Context, names CustomName, format string, fsys afero.Fs) error {
 	// Sanity checks.
-	if err := utils.LoadConfigFS(fsys); err != nil {
+	if err := flags.LoadConfig(fsys); err != nil {
 		return err
 	}
 	if err := assertContainerHealthy(ctx, utils.DbId); err != nil {
diff --git a/internal/stop/stop.go b/internal/stop/stop.go
index 39c5e00e5..da98f1600 100644
--- a/internal/stop/stop.go
+++ b/internal/stop/stop.go
@@ -9,6 +9,7 @@ import (
 	"github.com/docker/docker/api/types/volume"
 	"github.com/spf13/afero"
 	"github.com/supabase/cli/internal/utils"
+	"github.com/supabase/cli/internal/utils/flags"
 )
 
 func Run(ctx context.Context, backup bool, projectId string, all bool, fsys afero.Fs) error {
@@ -17,7 +18,7 @@ func Run(ctx context.Context, backup bool, projectId string, all bool, fsys afer
 		// Sanity checks.
 		if len(projectId) > 0 {
 			utils.Config.ProjectId = projectId
-		} else if err := utils.LoadConfigFS(fsys); err != nil {
+		} else if err := flags.LoadConfig(fsys); err != nil {
 			return err
 		}
 		searchProjectIdFilter = utils.Config.ProjectId
diff --git a/internal/storage/cp/cp.go b/internal/storage/cp/cp.go
index e2e304ced..4ead44639 100644
--- a/internal/storage/cp/cp.go
+++ b/internal/storage/cp/cp.go
@@ -115,7 +115,6 @@ func UploadStorageObjectAll(ctx context.Context, api storage.StorageAPI, remoteP
 			return err
 		}
 	}
-	remote, _ := utils.Config.GetRemoteByProjectRef(flags.ProjectRef)
 	// Overwrites existing object when using --recursive flag
 	opts = append(opts, func(fo *storage.FileOptions) {
 		fo.Overwrite = true
@@ -154,7 +153,7 @@ func UploadStorageObjectAll(ctx context.Context, api storage.StorageAPI, remoteP
 				// Retry after creating bucket
 				if bucket, prefix := client.SplitBucketPrefix(dstPath); len(prefix) > 0 {
 					body := storage.CreateBucketRequest{Name: bucket}
-					if config, ok := remote.Storage.Buckets[bucket]; ok {
+					if config, ok := utils.Config.Storage.Buckets[bucket]; ok {
 						body.Public = config.Public
 						body.FileSizeLimit = int64(config.FileSizeLimit)
 						body.AllowedMimeTypes = config.AllowedMimeTypes
diff --git a/internal/utils/config.go b/internal/utils/config.go
index 3f89dc75c..06d42d443 100644
--- a/internal/utils/config.go
+++ b/internal/utils/config.go
@@ -2,7 +2,6 @@ package utils
 
 import (
 	_ "embed"
-	"fmt"
 	"io/fs"
 	"net"
 	"net/url"
@@ -101,17 +100,6 @@ func GetDockerIds() []string {
 
 var Config = config.NewConfig(config.WithHostname(GetHostname()))
 
-func LoadConfigFS(fsys afero.Fs) error {
-	if err := Config.Load("", NewRootFS(fsys)); err != nil {
-		if errors.Is(err, os.ErrNotExist) {
-			CmdSuggestion = fmt.Sprintf("Have you set up the project with %s?", Aqua("supabase init"))
-		}
-		return err
-	}
-	UpdateDockerIds()
-	return nil
-}
-
 // Adapts fs.FS to support absolute paths
 type rootFS struct {
 	fsys afero.Fs
diff --git a/internal/utils/flags/config_path.go b/internal/utils/flags/config_path.go
new file mode 100644
index 000000000..d0ed105c7
--- /dev/null
+++ b/internal/utils/flags/config_path.go
@@ -0,0 +1,22 @@
+package flags
+
+import (
+	"fmt"
+	"os"
+
+	"github.com/go-errors/errors"
+	"github.com/spf13/afero"
+	"github.com/supabase/cli/internal/utils"
+)
+
+func LoadConfig(fsys afero.Fs) error {
+	utils.Config.ProjectId = ProjectRef
+	if err := utils.Config.Load("", utils.NewRootFS(fsys)); err != nil {
+		if errors.Is(err, os.ErrNotExist) {
+			utils.CmdSuggestion = fmt.Sprintf("Have you set up the project with %s?", utils.Aqua("supabase init"))
+		}
+		return err
+	}
+	utils.UpdateDockerIds()
+	return nil
+}
diff --git a/internal/utils/flags/db_url.go b/internal/utils/flags/db_url.go
index 013453b86..04565939d 100644
--- a/internal/utils/flags/db_url.go
+++ b/internal/utils/flags/db_url.go
@@ -61,7 +61,7 @@ func ParseDatabaseConfig(flagSet *pflag.FlagSet, fsys afero.Fs) error {
 			DbConfig = *config
 		}
 	case local:
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := LoadConfig(fsys); err != nil {
 			return err
 		}
 		// Ignore other PG settings
@@ -71,10 +71,10 @@ func ParseDatabaseConfig(flagSet *pflag.FlagSet, fsys afero.Fs) error {
 		DbConfig.Password = utils.Config.Db.Password
 		DbConfig.Database = "postgres"
 	case linked:
-		if err := utils.LoadConfigFS(fsys); err != nil {
+		if err := LoadProjectRef(fsys); err != nil {
 			return err
 		}
-		if err := LoadProjectRef(fsys); err != nil {
+		if err := LoadConfig(fsys); err != nil {
 			return err
 		}
 		DbConfig = NewDbConfigWithPassword(ProjectRef)
diff --git a/pkg/config/config.go b/pkg/config/config.go
index 837f305a9..93cc252c9 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -136,8 +136,7 @@ type (
 
 	config struct {
 		baseConfig `mapstructure:",squash"`
-		Overrides  map[string]interface{} `toml:"remotes"`
-		Remotes    map[string]baseConfig  `toml:"-"`
+		Remotes    map[string]baseConfig `toml:"remotes"`
 	}
 
 	realtime struct {
@@ -360,6 +359,7 @@ var (
 
 	invalidProjectId = regexp.MustCompile("[^a-zA-Z0-9_.-]+")
 	envPattern       = regexp.MustCompile(`^env\((.*)\)$`)
+	refPattern       = regexp.MustCompile(`^[a-z]{20}$`)
 )
 
 func (c *config) Eject(w io.Writer) error {
@@ -406,6 +406,24 @@ func (c *config) loadFromReader(v *viper.Viper, r io.Reader) error {
 	if err := v.MergeConfig(r); err != nil {
 		return errors.Errorf("failed to merge config: %w", err)
 	}
+	// Find [remotes.*] block to override base config
+	baseId := v.GetString("project_id")
+	idToName := map[string]string{baseId: "base"}
+	for name, remote := range v.GetStringMap("remotes") {
+		projectId := v.GetString(fmt.Sprintf("remotes.%s.project_id", name))
+		// Track remote project_id to check for duplication
+		if other, exists := idToName[projectId]; exists {
+			return errors.Errorf("duplicate project_id for [remotes.%s] and %s", name, other)
+		}
+		idToName[projectId] = fmt.Sprintf("[remotes.%s]", name)
+		if projectId == c.ProjectId {
+			fmt.Fprintln(os.Stderr, "Loading config override:", idToName[projectId])
+			if err := v.MergeConfigMap(remote.(map[string]any)); err != nil {
+				return err
+			}
+			v.Set("project_id", baseId)
+		}
+	}
 	// Manually parse [functions.*] to empty struct for backwards compatibility
 	for key, value := range v.GetStringMap("functions") {
 		if m, ok := value.(map[string]any); ok && len(m) == 0 {
@@ -532,50 +550,11 @@ func (c *config) Load(path string, fsys fs.FS) error {
 	if version, err := fs.ReadFile(fsys, builder.PgmetaVersionPath); err == nil && len(version) > 0 {
 		c.Studio.PgmetaImage = replaceImageTag(pgmetaImage, string(version))
 	}
-	// Resolve remote config, then base config
-	idToName := map[string]string{}
-	c.Remotes = make(map[string]baseConfig, len(c.Overrides))
-	for name, remote := range c.Overrides {
-		base := c.baseConfig.Clone()
-		// On remotes branches set seed as disabled by default
-		base.Db.Seed.Enabled = false
-		// Encode a toml file with only config overrides
-		var buf bytes.Buffer
-		if err := toml.NewEncoder(&buf).Encode(remote); err != nil {
-			return errors.Errorf("failed to encode map to TOML: %w", err)
-		}
-		// Decode overrides using base config as defaults
-		if metadata, err := toml.NewDecoder(&buf).Decode(&base); err != nil {
-			return errors.Errorf("failed to decode remote config: %w", err)
-		} else if undecoded := metadata.Undecoded(); len(undecoded) > 0 {
-			fmt.Fprintf(os.Stderr, "WARN: unknown config fields: %+v\n", undecoded)
-		}
-		// Cross validate remote project id
-		if base.ProjectId == c.baseConfig.ProjectId {
-			fmt.Fprintf(os.Stderr, "WARN: project_id is missing for [remotes.%s]\n", name)
-		} else if other, exists := idToName[base.ProjectId]; exists {
-			return errors.Errorf("duplicate project_id for [remotes.%s] and [remotes.%s]", other, name)
-		} else {
-			idToName[base.ProjectId] = name
-		}
-		if err := base.resolve(builder, fsys); err != nil {
-			return err
-		}
-		c.Remotes[name] = base
-	}
+	// TODO: replace derived config resolution with viper decode hooks
 	if err := c.baseConfig.resolve(builder, fsys); err != nil {
 		return err
 	}
-	// Validate base config, then remote config
-	if err := c.baseConfig.Validate(fsys); err != nil {
-		return err
-	}
-	for name, base := range c.Remotes {
-		if err := base.Validate(fsys); err != nil {
-			return errors.Errorf("invalid config for [remotes.%s]: %w", name, err)
-		}
-	}
-	return nil
+	return c.Validate(fsys)
 }
 
 func (c *baseConfig) resolve(builder pathBuilder, fsys fs.FS) error {
@@ -624,13 +603,19 @@ func (c *baseConfig) resolve(builder pathBuilder, fsys fs.FS) error {
 	return c.Db.Seed.loadSeedPaths(builder.SupabaseDirPath, fsys)
 }
 
-func (c *baseConfig) Validate(fsys fs.FS) error {
+func (c *config) Validate(fsys fs.FS) error {
 	if c.ProjectId == "" {
 		return errors.New("Missing required field in config: project_id")
 	} else if sanitized := sanitizeProjectId(c.ProjectId); sanitized != c.ProjectId {
 		fmt.Fprintln(os.Stderr, "WARN: project_id field in config is invalid. Auto-fixing to", sanitized)
 		c.ProjectId = sanitized
 	}
+	// Since remote config is merged to base, we only need to validate the project_id field.
+	for name, remote := range c.Remotes {
+		if !refPattern.MatchString(remote.ProjectId) {
+			return errors.Errorf("Invalid config for remotes.%s.project_id. Must be like: abcdefghijklmnopqrst", name)
+		}
+	}
 	// Validate api config
 	if c.Api.Enabled {
 		if c.Api.Port == 0 {
@@ -641,7 +626,7 @@ func (c *baseConfig) Validate(fsys fs.FS) error {
 	if c.Db.Settings.SessionReplicationRole != nil {
 		allowedRoles := []SessionReplicationRole{SessionReplicationRoleOrigin, SessionReplicationRoleReplica, SessionReplicationRoleLocal}
 		if !sliceContains(allowedRoles, *c.Db.Settings.SessionReplicationRole) {
-			return errors.Errorf("Invalid config for db.session_replication_role: %s. Must be one of: %v", *c.Db.Settings.SessionReplicationRole, allowedRoles)
+			return errors.Errorf("Invalid config for db.session_replication_role. Must be one of: %v", allowedRoles)
 		}
 	}
 	if c.Db.Port == 0 {
@@ -1328,25 +1313,16 @@ func (c *baseConfig) GetServiceImages() []string {
 }
 
 // Retrieve the final base config to use taking into account the remotes override
+// Pre: config must be loaded after setting config.ProjectID = "ref"
 func (c *config) GetRemoteByProjectRef(projectRef string) (baseConfig, error) {
-	var result []string
-	// Iterate over all the config.Remotes
-	for name, remoteConfig := range c.Remotes {
-		// Check if there is one matching project_id
-		if remoteConfig.ProjectId == projectRef {
-			// Check for duplicate project IDs across remotes
-			result = append(result, name)
+	base := c.baseConfig.Clone()
+	for _, remote := range c.Remotes {
+		if remote.ProjectId == projectRef {
+			base.ProjectId = projectRef
+			return base, nil
 		}
 	}
-	// If no matching remote config is found, return the base config
-	if len(result) == 0 {
-		return c.baseConfig, errors.Errorf("no remote found for project_id: %s", projectRef)
-	}
-	remote := c.Remotes[result[0]]
-	if len(result) > 1 {
-		return remote, errors.Errorf("multiple remotes %v have the same project_id: %s", result, projectRef)
-	}
-	return remote, nil
+	return base, errors.Errorf("no remote found for project_id: %s", projectRef)
 }
 
 func ToTomlBytes(config any) ([]byte, error) {
diff --git a/pkg/config/config_test.go b/pkg/config/config_test.go
index 45b2d04f6..2280ae40b 100644
--- a/pkg/config/config_test.go
+++ b/pkg/config/config_test.go
@@ -88,7 +88,7 @@ func TestConfigParsing(t *testing.T) {
 		staging, ok := config.Remotes["staging"]
 		assert.True(t, ok)
 		// Check the values for production override
-		assert.Equal(t, config.ProjectId, production.ProjectId)
+		assert.Equal(t, "vpefcjyosynxeiebfscx", production.ProjectId)
 		assert.Equal(t, "http://feature-auth-branch.com/", production.Auth.SiteUrl)
 		assert.Equal(t, false, production.Auth.EnableSignup)
 		assert.Equal(t, false, production.Auth.External["azure"].Enabled)
@@ -96,7 +96,7 @@ func TestConfigParsing(t *testing.T) {
 		// Check seed should be disabled by default for remote configs
 		assert.Equal(t, false, production.Db.Seed.Enabled)
 		// Check the values for the staging override
-		assert.Equal(t, "staging-project", staging.ProjectId)
+		assert.Equal(t, "bvikqvbczudanvggcord", staging.ProjectId)
 		assert.Equal(t, []string{"image/png"}, staging.Storage.Buckets["images"].AllowedMimeTypes)
 		assert.Equal(t, true, staging.Db.Seed.Enabled)
 	})
@@ -386,7 +386,7 @@ func TestLoadFunctionImportMap(t *testing.T) {
 		config := NewConfig()
 		fsys := fs.MapFS{
 			"supabase/config.toml": &fs.MapFile{Data: []byte(`
-			project_id = "test"
+			project_id = "bvikqvbczudanvggcord"
 			[functions.hello]
 			`)},
 			"supabase/functions/hello/deno.json": &fs.MapFile{},
@@ -402,7 +402,7 @@ func TestLoadFunctionImportMap(t *testing.T) {
 		config := NewConfig()
 		fsys := fs.MapFS{
 			"supabase/config.toml": &fs.MapFile{Data: []byte(`
-			project_id = "test"
+			project_id = "bvikqvbczudanvggcord"
 			[functions.hello]
 			`)},
 			"supabase/functions/hello/deno.jsonc": &fs.MapFile{},
@@ -418,7 +418,7 @@ func TestLoadFunctionImportMap(t *testing.T) {
 		config := NewConfig()
 		fsys := fs.MapFS{
 			"supabase/config.toml": &fs.MapFile{Data: []byte(`
-			project_id = "test"
+			project_id = "bvikqvbczudanvggcord"
 			[functions]
 			hello.import_map = "custom_import_map.json"
 			`)},
diff --git a/pkg/config/testdata/config.toml b/pkg/config/testdata/config.toml
index e3093924a..65705646c 100644
--- a/pkg/config/testdata/config.toml
+++ b/pkg/config/testdata/config.toml
@@ -251,6 +251,9 @@ s3_access_key = ""
 # Configures AWS_SECRET_ACCESS_KEY for S3 bucket
 s3_secret_key = ""
 
+[remotes.production]
+project_id = "vpefcjyosynxeiebfscx"
+
 [remotes.production.auth]
 site_url = "http://feature-auth-branch.com/"
 enable_signup = false
@@ -260,7 +263,7 @@ enabled = false
 client_id = "nope"
 
 [remotes.staging]
-project_id = "staging-project"
+project_id = "bvikqvbczudanvggcord"
 
 [remotes.staging.db.seed]
 enabled = true