diff --git a/internal/impl/io/input_streaming_file.go b/internal/impl/io/input_streaming_file.go
index b43efff32b..3be85c952d 100644
--- a/internal/impl/io/input_streaming_file.go
+++ b/internal/impl/io/input_streaming_file.go
@@ -61,7 +61,6 @@ type StreamingFileInputConfig struct {
 	MaxBufferSize      int           `json:"max_buffer_size"`
 	MaxLineSize        int           `json:"max_line_size"`
 	ReadTimeout        time.Duration `json:"read_timeout"`
-	ShutdownTimeout    time.Duration `json:"shutdown_timeout"`
 	Debug              bool          `json:"debug"`
 }
 
@@ -155,9 +154,6 @@ func NewStreamingFileInput(cfg StreamingFileInputConfig, logger *service.Logger)
 	if cfg.ReadTimeout <= 0 {
 		cfg.ReadTimeout = 30 * time.Second
 	}
-	if cfg.ShutdownTimeout <= 0 {
-		cfg.ShutdownTimeout = 30 * time.Second
-	}
 
 	if err := os.MkdirAll(cfg.StateDir, 0755); err != nil {
 		return nil, fmt.Errorf("failed to create state directory: %w", err)
@@ -1126,11 +1122,8 @@ func (sfi *StreamingFileInput) Close(ctx context.Context) error {
 		close(sfi.buffer)
 	}
 
-	shutdownTimeout := 30 * time.Second
-	if sfi.config.ShutdownTimeout > 0 {
-		shutdownTimeout = sfi.config.ShutdownTimeout
-	}
-
+	// Wait for in-flight messages to be acknowledged, respecting the context deadline
+	// which is controlled by Bento's shutdown_timeout configuration
 	drainDone := make(chan struct{})
 	go func() {
 		ticker := time.NewTicker(100 * time.Millisecond)
@@ -1152,24 +1145,22 @@ func (sfi *StreamingFileInput) Close(ctx context.Context) error {
 	select {
 	case <-drainDone:
 		sfi.logInfof("All in-flight messages acknowledged")
-	case <-time.After(shutdownTimeout):
+	case <-ctx.Done():
 		remaining := sfi.inFlightCount.Load()
-		sfi.logErrorf("CRITICAL: Shutdown timeout with %d in-flight messages. Persisting soft checkpoint.", remaining)
-		if sfi.metrics.ErrorsCounter != nil {
-			sfi.metrics.ErrorsCounter.Add(context.Background(), remaining,
-				metric.WithAttributes(
-					attribute.String("error_type", "shutdown_timeout"),
-					attribute.String("file", sfi.config.Path)))
-		}
-		softCtx, cancel := context.WithTimeout(context.Background(), 2*time.Second)
-		defer cancel()
-		if err := sfi.savePositionDurable(softCtx); err != nil {
-			sfi.logWarnf("Failed to persist soft checkpoint on shutdown timeout: %v", err)
-		} else {
-			sfi.logInfof("Soft checkpoint persisted with %d in-flight messages", remaining)
+		if remaining > 0 {
+			sfi.logWarnf("Shutdown with %d in-flight messages, persisting checkpoint", remaining)
+			if sfi.metrics.ErrorsCounter != nil {
+				sfi.metrics.ErrorsCounter.Add(context.Background(), remaining,
+					metric.WithAttributes(
+						attribute.String("error_type", "shutdown_timeout"),
+						attribute.String("file", sfi.config.Path)))
+			}
+			softCtx, cancel := context.WithTimeout(context.Background(), 2*time.Second)
+			if err := sfi.savePositionDurable(softCtx); err != nil {
+				sfi.logWarnf("Failed to persist checkpoint on shutdown: %v", err)
+			}
+			cancel()
 		}
-	case <-ctx.Done():
-		sfi.logWarnf("Close context cancelled with %d in-flight messages", sfi.inFlightCount.Load())
 	}
 
 	sfi.wg.Wait()