diff --git a/server/internal/desktop/clipboard.go b/server/internal/desktop/clipboard.go
index b67ecff0..fff20d8b 100644
--- a/server/internal/desktop/clipboard.go
+++ b/server/internal/desktop/clipboard.go
@@ -58,6 +58,23 @@ func (manager *DesktopManagerCtx) ClipboardGetBinary(mime string) ([]byte, error
 	return stdout.Bytes(), nil
 }
 
+func (manager *DesktopManagerCtx) replaceClipboardCommand(newCmd *exec.Cmd) {
+	// Swap the current clipboard command with the new one.
+	oldCmd := manager.clipboardCommand.Swap(newCmd)
+
+	// If the command is already running, we need to shutdown it properly.
+	if oldCmd == nil || oldCmd.ProcessState != nil {
+		return
+	}
+
+	// If there is a previous command running and it was not stopped yet, we need to kill it.
+	if err := oldCmd.Process.Kill(); err != nil {
+		manager.logger.Err(err).Msg("failed to kill previous clipboard command")
+	} else {
+		manager.logger.Debug().Msg("killed previous clipboard command")
+	}
+}
+
 func (manager *DesktopManagerCtx) ClipboardSetBinary(mime string, data []byte) error {
 	cmd := exec.Command("xclip", "-selection", "clipboard", "-in", "-target", mime)
 
@@ -69,7 +86,9 @@ func (manager *DesktopManagerCtx) ClipboardSetBinary(mime string, data []byte) e
 		return err
 	}
 
-	// TODO: Refactor.
+	// Shutdown previous command if it exists and replace it with the new one.
+	manager.replaceClipboardCommand(cmd)
+
 	// We need to wait until the data came to the clipboard.
 	wait := make(chan struct{})
 	xevent.Emmiter.Once("clipboard-updated", func(payload ...any) {
@@ -89,9 +108,23 @@ func (manager *DesktopManagerCtx) ClipboardSetBinary(mime string, data []byte) e
 
 	stdin.Close()
 
-	// TODO: Refactor.
-	// cmd.Wait()
-	<-wait
+	select {
+	case <-manager.shutdown:
+		return fmt.Errorf("clipboard manager is shutting down")
+	case <-wait:
+	}
+
+	manager.wg.Add(1)
+	go func() {
+		defer manager.wg.Done()
+
+		if err := cmd.Wait(); err != nil {
+			msg := strings.TrimSpace(stderr.String())
+			manager.logger.Err(err).Msgf("clipboard command finished with error: %s", msg)
+		} else {
+			manager.logger.Debug().Msg("clipboard command finished successfully")
+		}
+	}()
 
 	return nil
 }
diff --git a/server/internal/desktop/manager.go b/server/internal/desktop/manager.go
index 0ffadd73..aca5fe1a 100644
--- a/server/internal/desktop/manager.go
+++ b/server/internal/desktop/manager.go
@@ -1,7 +1,9 @@
 package desktop
 
 import (
+	"os/exec"
 	"sync"
+	"sync/atomic"
 	"time"
 
 	"github.com/kataras/go-events"
@@ -25,6 +27,11 @@ type DesktopManagerCtx struct {
 	config     *config.Desktop
 	screenSize types.ScreenSize // cached screen size
 	input      xinput.Driver
+
+	// Clipboard process holding the most recent clipboard data.
+	// It must remain running to allow pasting clipboard data.
+	// The last command is kept running until it is replaced or shutdown.
+	clipboardCommand atomic.Pointer[exec.Cmd]
 }
 
 func New(config *config.Desktop) *DesktopManagerCtx {
@@ -131,6 +138,8 @@ func (manager *DesktopManagerCtx) Shutdown() error {
 	manager.logger.Info().Msgf("shutdown")
 
 	close(manager.shutdown)
+
+	manager.replaceClipboardCommand(nil)
 	manager.wg.Wait()
 
 	xorg.DisplayClose()