diff --git a/extension/storage/filestorage/README.md b/extension/storage/filestorage/README.md
index c1a6bb5a9b4d..1ea12d91fb14 100644
--- a/extension/storage/filestorage/README.md
+++ b/extension/storage/filestorage/README.md
@@ -34,6 +34,10 @@ The default timeout is `1s`.
 `compaction.max_transaction_size` (default: 65536): defines maximum size of the compaction transaction.
 A value of zero will ignore transaction sizes.
 
+`compaction.cleanup_on_start` (default: false) - specifies if removal of compaction temporary files is performed on start.
+It will remove all the files in the compaction directory starting with tempdb,
+temp files will be left if a previous run of the process is killed while compacting.
+
 ### Rebound (online) compaction
 
 For rebound compaction, there are two additional parameters available:
diff --git a/extension/storage/filestorage/client.go b/extension/storage/filestorage/client.go
index c8fca4ba0201..1496ca14d464 100644
--- a/extension/storage/filestorage/client.go
+++ b/extension/storage/filestorage/client.go
@@ -8,6 +8,7 @@ import (
 	"errors"
 	"fmt"
 	"os"
+	"path/filepath"
 	"sync"
 	"syscall"
 	"time"
@@ -63,6 +64,9 @@ func newClient(logger *zap.Logger, filePath string, timeout time.Duration, compa
 	}
 
 	client := &fileStorageClient{logger: logger, db: db, compactionCfg: compactionCfg, openTimeout: timeout}
+	if compactionCfg.CleanupOnStart {
+		client.cleanup(compactionCfg.Directory)
+	}
 	if compactionCfg.OnRebound {
 		client.startCompactionLoop(context.Background())
 	}
@@ -342,3 +346,32 @@ func moveFileWithFallback(src string, dest string) error {
 	err = os.Remove(src)
 	return err
 }
+
+// cleanup left compaction temporary files from previous killed process
+func (c *fileStorageClient) cleanup(compactionDirectory string) error {
+	pattern := filepath.Join(compactionDirectory, "tempdb*")
+	contents, err := filepath.Glob(pattern)
+	if err != nil {
+		return err
+	}
+	delCont := 0
+	lockedCont := 0
+	for _, item := range contents {
+		err = os.Remove(item)
+		if err == nil {
+			delCont++
+			c.logger.Debug("cleanup",
+				zap.String("deletedFile", item))
+		} else {
+			lockedCont++
+			c.logger.Debug("cleanup",
+				zap.String("lockedFile", item),
+				zap.Error(err))
+		}
+
+	}
+	c.logger.Info("cleanup summary",
+		zap.Int("deletedFiles", delCont),
+		zap.Int("lockedFiles", lockedCont))
+	return nil
+}
diff --git a/extension/storage/filestorage/client_test.go b/extension/storage/filestorage/client_test.go
index 8717f553b90e..16b47f8cbfd0 100644
--- a/extension/storage/filestorage/client_test.go
+++ b/extension/storage/filestorage/client_test.go
@@ -404,6 +404,34 @@ func TestClientConcurrentCompaction(t *testing.T) {
 	}
 }
 
+func TestClientCleanupOnStart(t *testing.T) {
+	tempDir := t.TempDir()
+	dbFile := filepath.Join(tempDir, "my_db")
+	temp, _ := os.CreateTemp(tempDir, "tempdb")
+	// simulate ongoing compaction in another instance
+	tempLocked, _ := os.CreateTemp(tempDir, "tempdb")
+	temp.Close()
+
+	client, err := newClient(zap.NewNop(), dbFile, time.Second, &CompactionConfig{
+		Directory:      tempDir,
+		CleanupOnStart: true,
+	}, false)
+	require.NoError(t, err)
+
+	t.Cleanup(func() {
+		require.NoError(t, client.Close(context.TODO()))
+		tempLocked.Close()
+	})
+
+	// check if cleanup removed the unlocked file and left db and locked file
+	files, err := os.ReadDir(tempDir)
+	require.NoError(t, err)
+	require.Equal(t, 2, len(files))
+	require.Equal(t, "my_db", files[0].Name())
+	_, f := filepath.Split(tempLocked.Name())
+	require.Equal(t, f, files[1].Name())
+}
+
 func BenchmarkClientGet(b *testing.B) {
 	tempDir := b.TempDir()
 	dbFile := filepath.Join(tempDir, "my_db")
diff --git a/extension/storage/filestorage/config.go b/extension/storage/filestorage/config.go
index d71bbe0234fc..19e288a7655b 100644
--- a/extension/storage/filestorage/config.go
+++ b/extension/storage/filestorage/config.go
@@ -45,6 +45,10 @@ type CompactionConfig struct {
 	MaxTransactionSize int64 `mapstructure:"max_transaction_size,omitempty"`
 	// CheckInterval specifies frequency of compaction check
 	CheckInterval time.Duration `mapstructure:"check_interval,omitempty"`
+	// CleanupOnStart specifies removal of temporary files is performed on start.
+	// It will remove all the files in the compaction directory starting with tempdb,
+	// temp files will be left if a previous run of the process is killed while compacting.
+	CleanupOnStart bool `mapstructure:"cleanup_on_start,omitempty"`
 }
 
 func (cfg *Config) Validate() error {
diff --git a/extension/storage/filestorage/config_test.go b/extension/storage/filestorage/config_test.go
index 11d898a55f17..67decc8dbed5 100644
--- a/extension/storage/filestorage/config_test.go
+++ b/extension/storage/filestorage/config_test.go
@@ -45,6 +45,7 @@ func TestLoadConfig(t *testing.T) {
 					ReboundTriggerThresholdMiB: 16,
 					ReboundNeededThresholdMiB:  128,
 					CheckInterval:              time.Second * 5,
+					CleanupOnStart:             true,
 				},
 				Timeout: 2 * time.Second,
 				FSync:   true,
diff --git a/extension/storage/filestorage/extension_test.go b/extension/storage/filestorage/extension_test.go
index d808647b1293..cd4bf16f77fb 100644
--- a/extension/storage/filestorage/extension_test.go
+++ b/extension/storage/filestorage/extension_test.go
@@ -448,3 +448,38 @@ func TestCompactionRemoveTemp(t *testing.T) {
 	require.NoError(t, err)
 	require.Equal(t, 0, len(files))
 }
+
+func TestCleanupOnStart(t *testing.T) {
+	ctx := context.Background()
+
+	tempDir := t.TempDir()
+	// simulate left temporary compaction file from killed process
+	temp, _ := os.CreateTemp(tempDir, "tempdb")
+	temp.Close()
+
+	f := NewFactory()
+	cfg := f.CreateDefaultConfig().(*Config)
+	cfg.Directory = tempDir
+	cfg.Compaction.Directory = tempDir
+	cfg.Compaction.CleanupOnStart = true
+	extension, err := f.CreateExtension(context.Background(), extensiontest.NewNopCreateSettings(), cfg)
+	require.NoError(t, err)
+
+	se, ok := extension.(storage.Extension)
+	require.True(t, ok)
+
+	client, err := se.GetClient(
+		ctx,
+		component.KindReceiver,
+		newTestEntity("my_component"),
+		"",
+	)
+	require.NoError(t, err)
+	t.Cleanup(func() {
+		require.NoError(t, client.Close(ctx))
+	})
+
+	files, err := os.ReadDir(tempDir)
+	require.NoError(t, err)
+	require.Equal(t, 1, len(files))
+}
diff --git a/extension/storage/filestorage/factory.go b/extension/storage/filestorage/factory.go
index ef3e04e9d3c7..18178c54a4ea 100644
--- a/extension/storage/filestorage/factory.go
+++ b/extension/storage/filestorage/factory.go
@@ -45,6 +45,7 @@ func createDefaultConfig() component.Config {
 			ReboundNeededThresholdMiB:  defaultReboundNeededThresholdMib,
 			ReboundTriggerThresholdMiB: defaultReboundTriggerThresholdMib,
 			CheckInterval:              defaultCompactionInterval,
+			CleanupOnStart:             false,
 		},
 		Timeout: time.Second,
 		FSync:   false,
diff --git a/extension/storage/filestorage/testdata/config.yaml b/extension/storage/filestorage/testdata/config.yaml
index 4a923aee71fe..bcdbaac9a291 100644
--- a/extension/storage/filestorage/testdata/config.yaml
+++ b/extension/storage/filestorage/testdata/config.yaml
@@ -12,5 +12,6 @@ file_storage/all_settings:
     rebound_trigger_threshold_mib: 16
     rebound_needed_threshold_mib: 128
     max_transaction_size: 2048
+    cleanup_on_start: true
   timeout: 2s
   fsync: true