diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3b56837dd03..a2c3d40e931 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
 - We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
 - We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)
 
diff --git a/src/main/java/org/jabref/JabRefExecutorService.java b/src/main/java/org/jabref/JabRefExecutorService.java
index a90668d9bd2..0820bf196bc 100644
--- a/src/main/java/org/jabref/JabRefExecutorService.java
+++ b/src/main/java/org/jabref/JabRefExecutorService.java
@@ -22,24 +22,29 @@
 public class JabRefExecutorService {
 
     public static final JabRefExecutorService INSTANCE = new JabRefExecutorService();
+
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefExecutorService.class);
+
     private final ExecutorService executorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef CachedThreadPool");
         thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         return thread;
     });
+
     private final ExecutorService lowPriorityExecutorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef LowPriorityCachedThreadPool");
         thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         return thread;
     });
+
     private final Timer timer = new Timer("timer", true);
+
     private Thread remoteThread;
 
     private JabRefExecutorService() {
-    }
+   }
 
     public void execute(Runnable command) {
         Objects.requireNonNull(command);
@@ -132,13 +137,16 @@ public void submit(TimerTask timerTask, long millisecondsDelay) {
         timer.schedule(timerTask, millisecondsDelay);
     }
 
+    /**
+     * Shuts everything down. After termination, this method returns.
+     */
     public void shutdownEverything() {
-        // those threads will be allowed to finish
-        this.executorService.shutdown();
-        // those threads will be interrupted in their current task
-        this.lowPriorityExecutorService.shutdownNow();
         // kill the remote thread
         stopRemoteThread();
+
+        gracefullyShutdown(this.executorService);
+        gracefullyShutdown(this.lowPriorityExecutorService);
+
         timer.cancel();
     }
 
@@ -164,4 +172,28 @@ public void run() {
             }
         }
     }
+
+    /**
+     * Shuts down the provided executor service by first trying a normal shutdown, then waiting for the shutdown and then forcibly shutting it down.
+     * Returns if the status of the shut down is known.
+     */
+    public static void gracefullyShutdown(ExecutorService executorService) {
+        try {
+            // This is non-blocking. See https://stackoverflow.com/a/57383461/873282.
+            executorService.shutdown();
+            if (!executorService.awaitTermination(60, TimeUnit.SECONDS)) {
+                LOGGER.debug("One minute passed, {} still not completed. Trying forced shutdown.", executorService.toString());
+                // those threads will be interrupted in their current task
+                executorService.shutdownNow();
+                if (executorService.awaitTermination(60, TimeUnit.SECONDS)) {
+                    LOGGER.debug("One minute passed again - forced shutdown of {} worked.", executorService.toString());
+                } else {
+                    LOGGER.error("{} did not terminate", executorService.toString());
+                }
+            }
+        } catch (InterruptedException ie) {
+            executorService.shutdownNow();
+            Thread.currentThread().interrupt();
+        }
+    }
 }
diff --git a/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java b/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
index 6cbb6b27515..a6073dcad96 100644
--- a/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
+++ b/src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
@@ -122,6 +122,9 @@ public <V> Future<?> schedule(BackgroundTask<V> task, long delay, TimeUnit unit)
         return scheduledExecutor.schedule(getJavaFXTask(task), delay, unit);
     }
 
+    /**
+     * Shuts everything down. After termination, this method returns.
+     */
     @Override
     public void shutdown() {
         executor.shutdownNow();
diff --git a/src/main/java/org/jabref/gui/util/TaskExecutor.java b/src/main/java/org/jabref/gui/util/TaskExecutor.java
index f56d516eed6..e08d858a0cc 100644
--- a/src/main/java/org/jabref/gui/util/TaskExecutor.java
+++ b/src/main/java/org/jabref/gui/util/TaskExecutor.java
@@ -45,7 +45,7 @@ public interface TaskExecutor {
     <V> Future<?> schedule(BackgroundTask<V> task, long delay, TimeUnit unit);
 
     /**
-     * Shutdown the task executor.
+     * Shutdown the task executor. May happen in the background or may be finished when this method returns.
      */
     void shutdown();
 
diff --git a/src/main/java/org/jabref/logic/util/DelayTaskThrottler.java b/src/main/java/org/jabref/logic/util/DelayTaskThrottler.java
index 3b30027f5c3..fcb0c74551f 100644
--- a/src/main/java/org/jabref/logic/util/DelayTaskThrottler.java
+++ b/src/main/java/org/jabref/logic/util/DelayTaskThrottler.java
@@ -5,6 +5,8 @@
 import java.util.concurrent.ScheduledThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
+import org.jabref.JabRefExecutorService;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -32,6 +34,7 @@ public DelayTaskThrottler(int delay) {
         this.delay = delay;
         this.executor = new ScheduledThreadPoolExecutor(1);
         this.executor.setRemoveOnCancelPolicy(true);
+        this.executor.setExecuteExistingDelayedTasksAfterShutdownPolicy(false);
     }
 
     public void schedule(Runnable command) {
@@ -45,7 +48,10 @@ public void schedule(Runnable command) {
         }
     }
 
+    /**
+     * Shuts everything down. Upon termination, this method returns.
+     */
     public void shutdown() {
-        executor.shutdown();
+        JabRefExecutorService.gracefullyShutdown(executor);
     }
 }