diff --git a/internal/db/declarative/debug.go b/internal/db/declarative/debug.go
index f274ed39dd..30ffaa4c7b 100644
--- a/internal/db/declarative/debug.go
+++ b/internal/db/declarative/debug.go
@@ -104,9 +104,9 @@ func CollectMigrationsList(fsys afero.Fs) []string {
 	if err != nil {
 		return nil
 	}
-	// Strip directory prefix to return just filenames
+	// Strip directory prefix to return display names
 	for i, m := range migrations {
-		migrations[i] = filepath.Base(m)
+		migrations[i] = migration.MigrationName(m)
 	}
 	return migrations
 }
diff --git a/internal/db/push/push.go b/internal/db/push/push.go
index 4084cd0800..79af124f33 100644
--- a/internal/db/push/push.go
+++ b/internal/db/push/push.go
@@ -4,7 +4,6 @@ import (
 	"context"
 	"fmt"
 	"os"
-	"path/filepath"
 
 	"github.com/go-errors/errors"
 	"github.com/jackc/pgconn"
@@ -118,8 +117,7 @@ func Run(ctx context.Context, dryRun, ignoreVersionMismatch bool, includeRoles,
 
 func confirmPushAll(pending []string) (msg string) {
 	for _, path := range pending {
-		filename := filepath.Base(path)
-		msg += fmt.Sprintf(" • %s\n", utils.Bold(filename))
+		msg += fmt.Sprintf(" • %s\n", utils.Bold(migration.MigrationName(path)))
 	}
 	return msg
 }
diff --git a/internal/migration/repair/repair.go b/internal/migration/repair/repair.go
index a7dfee274e..1ab6fd34d6 100644
--- a/internal/migration/repair/repair.go
+++ b/internal/migration/repair/repair.go
@@ -88,15 +88,28 @@ func UpdateMigrationTable(ctx context.Context, conn *pgx.Conn, version []string,
 }
 
 func GetMigrationFile(version string, fsys afero.Fs) (string, error) {
+	// Try flat file first: version_*.sql
 	path := filepath.Join(utils.MigrationsDir, version+"_*.sql")
 	matches, err := afero.Glob(fsys, path)
 	if err != nil {
 		return "", errors.Errorf("failed to glob migration files: %w", err)
 	}
-	if len(matches) == 0 {
-		return "", errors.Errorf("glob %s: %w", path, os.ErrNotExist)
+	if len(matches) > 0 {
+		return matches[0], nil
 	}
-	return matches[0], nil
+	// Try folder-based migration: version_*/*.sql
+	dirPath := filepath.Join(utils.MigrationsDir, version+"_*", "*.sql")
+	dirMatches, err := afero.Glob(fsys, dirPath)
+	if err != nil {
+		return "", errors.Errorf("failed to glob migration directories: %w", err)
+	}
+	if len(dirMatches) == 1 {
+		return dirMatches[0], nil
+	}
+	if len(dirMatches) > 1 {
+		return "", errors.Errorf("multiple .sql files found for version %s", version)
+	}
+	return "", errors.Errorf("no migration found for version %s: %w", version, os.ErrNotExist)
 }
 
 func NewMigrationFromVersion(version string, fsys afero.Fs) (*migration.MigrationFile, error) {
diff --git a/internal/migration/repair/repair_test.go b/internal/migration/repair/repair_test.go
index f8eb33cce8..b415069c5d 100644
--- a/internal/migration/repair/repair_test.go
+++ b/internal/migration/repair/repair_test.go
@@ -61,6 +61,23 @@ func TestRepairCommand(t *testing.T) {
 		assert.NoError(t, err)
 	})
 
+	t.Run("applies folder-based migration version", func(t *testing.T) {
+		// Setup in-memory fs
+		fsys := afero.NewMemMapFs()
+		sqlPath := filepath.Join(utils.MigrationsDir, "20242409125510_premium_mister_fear", "schema.sql")
+		require.NoError(t, afero.WriteFile(fsys, sqlPath, []byte("select 1"), 0644))
+		// Setup mock postgres
+		conn := pgtest.NewConn()
+		defer conn.Close(t)
+		helper.MockMigrationHistory(conn).
+			Query(migration.UPSERT_MIGRATION_VERSION, "20242409125510", "premium_mister_fear", []string{"select 1"}).
+			Reply("INSERT 0 1")
+		// Run test
+		err := Run(context.Background(), dbConfig, []string{"20242409125510"}, Applied, fsys, conn.Intercept)
+		// Check error
+		assert.NoError(t, err)
+	})
+
 	t.Run("throws error on invalid version", func(t *testing.T) {
 		// Setup in-memory fs
 		fsys := afero.NewMemMapFs()
@@ -97,6 +114,45 @@ func TestRepairCommand(t *testing.T) {
 	})
 }
 
+func TestGetMigrationFile(t *testing.T) {
+	t.Run("finds flat migration file", func(t *testing.T) {
+		fsys := afero.NewMemMapFs()
+		path := filepath.Join(utils.MigrationsDir, "0_test.sql")
+		require.NoError(t, afero.WriteFile(fsys, path, []byte("select 1"), 0644))
+		// Run test
+		result, err := GetMigrationFile("0", fsys)
+		assert.NoError(t, err)
+		assert.Equal(t, path, result)
+	})
+
+	t.Run("finds folder-based migration file", func(t *testing.T) {
+		fsys := afero.NewMemMapFs()
+		sqlPath := filepath.Join(utils.MigrationsDir, "20242409125510_premium_mister_fear", "schema.sql")
+		require.NoError(t, afero.WriteFile(fsys, sqlPath, []byte("select 1"), 0644))
+		// Run test
+		result, err := GetMigrationFile("20242409125510", fsys)
+		assert.NoError(t, err)
+		assert.Equal(t, sqlPath, result)
+	})
+
+	t.Run("returns error for multiple .sql files in directory", func(t *testing.T) {
+		fsys := afero.NewMemMapFs()
+		dir := filepath.Join(utils.MigrationsDir, "20242409125510_premium_mister_fear")
+		require.NoError(t, afero.WriteFile(fsys, filepath.Join(dir, "schema.sql"), []byte("select 1"), 0644))
+		require.NoError(t, afero.WriteFile(fsys, filepath.Join(dir, "extra.sql"), []byte("select 2"), 0644))
+		// Run test
+		_, err := GetMigrationFile("20242409125510", fsys)
+		assert.ErrorContains(t, err, "multiple .sql files found")
+	})
+
+	t.Run("returns error when version not found", func(t *testing.T) {
+		fsys := afero.NewMemMapFs()
+		// Run test
+		_, err := GetMigrationFile("99999", fsys)
+		assert.ErrorIs(t, err, os.ErrNotExist)
+	})
+}
+
 func TestRepairAll(t *testing.T) {
 	t.Run("repairs whole history", func(t *testing.T) {
 		t.Cleanup(fstest.MockStdin(t, "y"))
diff --git a/internal/migration/squash/squash.go b/internal/migration/squash/squash.go
index afc52c687e..53e63e9494 100644
--- a/internal/migration/squash/squash.go
+++ b/internal/migration/squash/squash.go
@@ -7,6 +7,7 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"path/filepath"
 	"strconv"
 	"time"
 
@@ -73,6 +74,14 @@ func squashToVersion(ctx context.Context, version string, fsys afero.Fs, options
 	for _, path := range migrations[:len(migrations)-1] {
 		if err := fsys.Remove(path); err != nil {
 			fmt.Fprintln(os.Stderr, err)
+			continue
+		}
+		// For folder-based migrations, remove the parent directory and all its contents
+		dir := filepath.Dir(path)
+		if dir != utils.MigrationsDir {
+			if err := fsys.RemoveAll(dir); err != nil {
+				fmt.Fprintln(os.Stderr, err)
+			}
 		}
 	}
 	return nil
diff --git a/pkg/migration/apply.go b/pkg/migration/apply.go
index e40b58be2e..80cdebc487 100644
--- a/pkg/migration/apply.go
+++ b/pkg/migration/apply.go
@@ -5,7 +5,6 @@ import (
 	"fmt"
 	"io/fs"
 	"os"
-	"path/filepath"
 
 	"github.com/go-errors/errors"
 	"github.com/jackc/pgx/v4"
@@ -23,9 +22,8 @@ func FindPendingMigrations(localMigrations, remoteMigrations []string) ([]string
 	i, j := 0, 0
 	for i < len(remoteMigrations) && j < len(localMigrations) {
 		remote := remoteMigrations[i]
-		filename := filepath.Base(localMigrations[j])
-		// Check if migration has been applied before, LoadLocalMigrations guarantees a match
-		local := migrateFilePattern.FindStringSubmatch(filename)[1]
+		// Extract version from path, supporting both flat files and folder-based migrations
+		local, _, _ := ParseVersion(localMigrations[j])
 		if remote == local {
 			j++
 			i++
@@ -60,8 +58,7 @@ func ApplyMigrations(ctx context.Context, pending []string, conn *pgx.Conn, fsys
 		}
 	}
 	for _, path := range pending {
-		filename := filepath.Base(path)
-		fmt.Fprintf(os.Stderr, "Applying migration %s...\n", filename)
+		fmt.Fprintf(os.Stderr, "Applying migration %s...\n", MigrationName(path))
 		// Reset all connection settings that might have been modified by another statement on the same connection
 		// eg: `SELECT pg_catalog.set_config('search_path', '', false);`
 		if _, err := conn.Exec(ctx, "RESET ALL"); err != nil {
diff --git a/pkg/migration/apply_test.go b/pkg/migration/apply_test.go
index e6df97721f..6fbe43e806 100644
--- a/pkg/migration/apply_test.go
+++ b/pkg/migration/apply_test.go
@@ -91,6 +91,55 @@ func TestPendingMigrations(t *testing.T) {
 		assert.ErrorIs(t, err, ErrMissingLocal)
 		assert.ElementsMatch(t, []string{remote[1], remote[3], remote[4]}, missing)
 	})
+
+	t.Run("finds pending folder-based migrations", func(t *testing.T) {
+		local := []string{
+			"20221201000000_test.sql",
+			"20221201000001_test.sql",
+			"20221201000002_create_users/schema.sql",
+			"20221201000003_add_indexes/schema.sql",
+		}
+		remote := []string{
+			"20221201000000",
+			"20221201000001",
+		}
+		// Run test
+		pending, err := FindPendingMigrations(local, remote)
+		// Check error
+		assert.NoError(t, err)
+		assert.ElementsMatch(t, local[2:], pending)
+	})
+
+	t.Run("matches remote with local folder-based migration", func(t *testing.T) {
+		local := []string{
+			"20221201000000_test.sql",
+			"20221201000001_create_users/schema.sql",
+		}
+		remote := []string{
+			"20221201000000",
+			"20221201000001",
+		}
+		// Run test
+		pending, err := FindPendingMigrations(local, remote)
+		// Check error
+		assert.NoError(t, err)
+		assert.Empty(t, pending)
+	})
+
+	t.Run("detects missing local for folder-based migrations", func(t *testing.T) {
+		local := []string{
+			"20221201000000_create_users/schema.sql",
+		}
+		remote := []string{
+			"20221201000000",
+			"20221201000001",
+		}
+		// Run test
+		missing, err := FindPendingMigrations(local, remote)
+		// Check error
+		assert.ErrorIs(t, err, ErrMissingLocal)
+		assert.ElementsMatch(t, []string{"20221201000001"}, missing)
+	})
 }
 
 var (
diff --git a/pkg/migration/file.go b/pkg/migration/file.go
index 540c129e33..674d32bb3c 100644
--- a/pkg/migration/file.go
+++ b/pkg/migration/file.go
@@ -28,6 +28,7 @@ type MigrationFile struct {
 
 var (
 	migrateFilePattern = regexp.MustCompile(`^([0-9]+)_(.*)\.sql$`)
+	migrateDirPattern  = regexp.MustCompile(`^([0-9]+)_(.+)$`)
 	typeNamePattern    = regexp.MustCompile(`type "([^"]+)" does not exist`)
 )
 
@@ -37,16 +38,43 @@ func NewMigrationFromFile(path string, fsys fs.FS) (*MigrationFile, error) {
 		return nil, err
 	}
 	file := MigrationFile{Statements: lines}
-	// Parse version from file name
-	filename := filepath.Base(path)
-	matches := migrateFilePattern.FindStringSubmatch(filename)
-	if len(matches) > 2 {
-		file.Version = matches[1]
-		file.Name = matches[2]
+	// Parse version from file path (supports both flat files and folder-based migrations)
+	if version, name, ok := ParseVersion(path); ok {
+		file.Version = version
+		file.Name = name
 	}
 	return &file, nil
 }
 
+// ParseVersion extracts the version and name from a migration path.
+// Handles both flat files (20220727064247_create_table.sql) and
+// folder-based migrations (20242409125510_premium_mister_fear/<file>.sql).
+func ParseVersion(path string) (version, name string, ok bool) {
+	filename := filepath.Base(path)
+	if matches := migrateFilePattern.FindStringSubmatch(filename); len(matches) > 2 {
+		return matches[1], matches[2], true
+	}
+	// Try parent directory for folder-based migrations
+	dirName := filepath.Base(filepath.Dir(path))
+	if matches := migrateDirPattern.FindStringSubmatch(dirName); len(matches) > 2 {
+		return matches[1], matches[2], true
+	}
+	return "", "", false
+}
+
+// MigrationName returns a human-readable display name for a migration path.
+// For flat files: "20220727064247_create_table.sql"
+// For folder migrations: "20242409125510_premium_mister_fear/<file>.sql"
+func MigrationName(path string) string {
+	filename := filepath.Base(path)
+	if migrateFilePattern.MatchString(filename) {
+		return filename
+	}
+	// For folder-based migrations, show "dirname/filename"
+	dir := filepath.Base(filepath.Dir(path))
+	return filepath.Join(dir, filename)
+}
+
 func parseFile(path string, fsys fs.FS) ([]string, error) {
 	sql, err := fsys.Open(path)
 	if err != nil {
diff --git a/pkg/migration/file_test.go b/pkg/migration/file_test.go
index 703f26954c..fd137725db 100644
--- a/pkg/migration/file_test.go
+++ b/pkg/migration/file_test.go
@@ -100,6 +100,21 @@ func TestMigrationFile(t *testing.T) {
 		assert.ErrorContains(t, err, "At statement: 0")
 	})
 
+	t.Run("new from folder-based migration", func(t *testing.T) {
+		// Setup in-memory fs
+		fsys := fs.MapFS{
+			"20242409125510_premium_mister_fear/schema.sql":   &fs.MapFile{Data: []byte("CREATE TABLE foo (id int)")},
+			"20242409125510_premium_mister_fear/snapshot.json": &fs.MapFile{Data: []byte("{}")},
+		}
+		// Run test
+		migration, err := NewMigrationFromFile("20242409125510_premium_mister_fear/schema.sql", fsys)
+		// Check error
+		assert.NoError(t, err)
+		assert.Equal(t, "20242409125510", migration.Version)
+		assert.Equal(t, "premium_mister_fear", migration.Name)
+		assert.Len(t, migration.Statements, 1)
+	})
+
 	t.Run("skips hint for schema-qualified type errors", func(t *testing.T) {
 		migration := MigrationFile{
 			Statements: []string{"CREATE TABLE test (path extensions.ltree NOT NULL)"},
@@ -158,3 +173,60 @@ func TestIsSchemaQualified(t *testing.T) {
 	assert.False(t, IsSchemaQualified("ltree"))
 	assert.False(t, IsSchemaQualified(""))
 }
+
+func TestParseVersion(t *testing.T) {
+	t.Run("extracts version from flat file", func(t *testing.T) {
+		version, name, ok := ParseVersion("20220727064247_create_table.sql")
+		assert.True(t, ok)
+		assert.Equal(t, "20220727064247", version)
+		assert.Equal(t, "create_table", name)
+	})
+
+	t.Run("extracts version from flat file with path", func(t *testing.T) {
+		version, name, ok := ParseVersion("supabase/migrations/20220727064247_create_table.sql")
+		assert.True(t, ok)
+		assert.Equal(t, "20220727064247", version)
+		assert.Equal(t, "create_table", name)
+	})
+
+	t.Run("extracts version from folder-based migration", func(t *testing.T) {
+		version, name, ok := ParseVersion("supabase/migrations/20242409125510_premium_mister_fear/schema.sql")
+		assert.True(t, ok)
+		assert.Equal(t, "20242409125510", version)
+		assert.Equal(t, "premium_mister_fear", name)
+	})
+
+	t.Run("extracts version from folder-based migration without parent path", func(t *testing.T) {
+		version, name, ok := ParseVersion("20242409125510_premium_mister_fear/schema.sql")
+		assert.True(t, ok)
+		assert.Equal(t, "20242409125510", version)
+		assert.Equal(t, "premium_mister_fear", name)
+	})
+
+	t.Run("returns false for non-matching path", func(t *testing.T) {
+		_, _, ok := ParseVersion("random_file.txt")
+		assert.False(t, ok)
+	})
+
+	t.Run("returns false for .sql without matching parent dir", func(t *testing.T) {
+		_, _, ok := ParseVersion("some_dir/schema.sql")
+		assert.False(t, ok)
+	})
+}
+
+func TestMigrationName(t *testing.T) {
+	t.Run("returns filename for flat migration", func(t *testing.T) {
+		assert.Equal(t, "20220727064247_create_table.sql", MigrationName("supabase/migrations/20220727064247_create_table.sql"))
+	})
+
+	t.Run("returns dir/file for folder-based migration", func(t *testing.T) {
+		assert.Equal(t,
+			"20242409125510_premium_mister_fear/schema.sql",
+			MigrationName("supabase/migrations/20242409125510_premium_mister_fear/schema.sql"),
+		)
+	})
+
+	t.Run("returns filename when no parent directory", func(t *testing.T) {
+		assert.Equal(t, "20220727064247_create_table.sql", MigrationName("20220727064247_create_table.sql"))
+	})
+}
diff --git a/pkg/migration/list.go b/pkg/migration/list.go
index 8972bb2594..ce36312a3b 100644
--- a/pkg/migration/list.go
+++ b/pkg/migration/list.go
@@ -37,23 +37,55 @@ func ListLocalMigrations(migrationsDir string, fsys fs.FS, filter ...func(string
 	}
 	var clean []string
 OUTER:
-	for i, migration := range localMigrations {
-		if migration.IsDir() {
-			continue
-		}
-		filename := migration.Name()
-		if i == 0 && shouldSkip(filename) {
-			fmt.Fprintf(os.Stderr, "Skipping migration %s... (replace \"init\" with a different file name to apply this migration)\n", filename)
-			continue
-		}
-		matches := migrateFilePattern.FindStringSubmatch(filename)
-		if len(matches) == 0 {
-			fmt.Fprintf(os.Stderr, "Skipping migration %s... (file name must match pattern \"<timestamp>_name.sql\")\n", filename)
-			continue
+	for i, entry := range localMigrations {
+		var path, version string
+
+		if entry.IsDir() {
+			dirName := entry.Name()
+			matches := migrateDirPattern.FindStringSubmatch(dirName)
+			if len(matches) == 0 {
+				continue
+			}
+			// Look for exactly one .sql file inside the directory
+			dirPath := filepath.Join(migrationsDir, dirName)
+			entries, err := fs.ReadDir(fsys, dirPath)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Skipping migration directory %s... (%v)\n", dirName, err)
+				continue
+			}
+			var sqlFiles []string
+			for _, e := range entries {
+				if !e.IsDir() && filepath.Ext(e.Name()) == ".sql" {
+					sqlFiles = append(sqlFiles, e.Name())
+				}
+			}
+			if len(sqlFiles) != 1 {
+				if len(sqlFiles) == 0 {
+					fmt.Fprintf(os.Stderr, "Skipping migration directory %s... (no .sql file found)\n", dirName)
+				} else {
+					fmt.Fprintf(os.Stderr, "Skipping migration directory %s... (multiple .sql files found)\n", dirName)
+				}
+				continue
+			}
+			path = filepath.Join(migrationsDir, dirName, sqlFiles[0])
+			version = matches[1]
+		} else {
+			filename := entry.Name()
+			if i == 0 && shouldSkip(filename) {
+				fmt.Fprintf(os.Stderr, "Skipping migration %s... (replace \"init\" with a different file name to apply this migration)\n", filename)
+				continue
+			}
+			matches := migrateFilePattern.FindStringSubmatch(filename)
+			if len(matches) == 0 {
+				fmt.Fprintf(os.Stderr, "Skipping migration %s... (file name must match pattern \"<timestamp>_name.sql\")\n", filename)
+				continue
+			}
+			path = filepath.Join(migrationsDir, filename)
+			version = matches[1]
 		}
-		path := filepath.Join(migrationsDir, filename)
+
 		for _, keep := range filter {
-			if version := matches[1]; !keep(version) {
+			if !keep(version) {
 				continue OUTER
 			}
 		}
diff --git a/pkg/migration/list_test.go b/pkg/migration/list_test.go
index 4654fa876a..afe0e61a0c 100644
--- a/pkg/migration/list_test.go
+++ b/pkg/migration/list_test.go
@@ -89,4 +89,58 @@ func TestLocalMigrations(t *testing.T) {
 		// Check error
 		assert.ErrorContains(t, err, "failed to read directory:")
 	})
+
+	t.Run("loads folder-based migrations", func(t *testing.T) {
+		// Setup in-memory fs
+		fsys := fs.MapFS{
+			"20220727064246_test.sql":                        &fs.MapFile{},
+			"20242409125510_premium_mister_fear/schema.sql":  &fs.MapFile{},
+			"20242409125510_premium_mister_fear/snapshot.json": &fs.MapFile{},
+		}
+		// Run test
+		versions, err := ListLocalMigrations(".", fsys)
+		// Check error
+		assert.NoError(t, err)
+		assert.Equal(t, []string{
+			"20220727064246_test.sql",
+			"20242409125510_premium_mister_fear/schema.sql",
+		}, versions)
+	})
+
+	t.Run("skips directory without .sql file", func(t *testing.T) {
+		// Setup in-memory fs — directory with only snapshot.json, no .sql file
+		fsys := fs.MapFS{
+			"20242409125510_premium_mister_fear/snapshot.json": &fs.MapFile{},
+		}
+		// Run test
+		versions, err := ListLocalMigrations(".", fsys)
+		// Check error
+		assert.NoError(t, err)
+		assert.Empty(t, versions)
+	})
+
+	t.Run("skips directory with multiple .sql files", func(t *testing.T) {
+		// Setup in-memory fs — directory with more than one .sql file
+		fsys := fs.MapFS{
+			"20242409125510_premium_mister_fear/schema.sql": &fs.MapFile{},
+			"20242409125510_premium_mister_fear/extra.sql":  &fs.MapFile{},
+		}
+		// Run test
+		versions, err := ListLocalMigrations(".", fsys)
+		// Check error
+		assert.NoError(t, err)
+		assert.Empty(t, versions)
+	})
+
+	t.Run("skips directory with non-matching name", func(t *testing.T) {
+		// Setup in-memory fs — directory name doesn't start with digits
+		fsys := fs.MapFS{
+			"some_random_dir/schema.sql": &fs.MapFile{},
+		}
+		// Run test
+		versions, err := ListLocalMigrations(".", fsys)
+		// Check error
+		assert.NoError(t, err)
+		assert.Empty(t, versions)
+	})
 }