diff --git a/jablib/src/main/java/org/jabref/logic/preferences/LastFilesOpenedPreferences.java b/jablib/src/main/java/org/jabref/logic/preferences/LastFilesOpenedPreferences.java
index f136c0aa64a..b5e69988ba3 100644
--- a/jablib/src/main/java/org/jabref/logic/preferences/LastFilesOpenedPreferences.java
+++ b/jablib/src/main/java/org/jabref/logic/preferences/LastFilesOpenedPreferences.java
@@ -21,13 +21,17 @@ public class LastFilesOpenedPreferences {
     private final FileHistory fileHistory;
 
     public LastFilesOpenedPreferences(List<Path> lastFilesOpened, Path lastFocusedFile, FileHistory fileHistory) {
-        this.lastFilesOpened = FXCollections.observableArrayList(lastFilesOpened);
-        this.lastFocusedFile = new SimpleObjectProperty<>(lastFocusedFile);
+        this.lastFilesOpened = FXCollections.observableArrayList(
+                lastFilesOpened.stream().map(this::toRelative).toList()
+        );
+        this.lastFocusedFile = new SimpleObjectProperty<>(toRelative(lastFocusedFile));
         this.fileHistory = fileHistory;
     }
 
     public ObservableList<Path> getLastFilesOpened() {
-        return lastFilesOpened;
+        return FXCollections.observableArrayList(
+                lastFilesOpened.stream().map(this::toAbsolute).toList()
+        );
     }
 
     public void setLastFilesOpened(List<Path> files) {
@@ -35,7 +39,7 @@ public void setLastFilesOpened(List<Path> files) {
     }
 
     public Path getLastFocusedFile() {
-        return lastFocusedFile.get();
+        return toAbsolute(lastFocusedFile.get());
     }
 
     public ObjectProperty<Path> lastFocusedFileProperty() {
@@ -43,10 +47,33 @@ public ObjectProperty<Path> lastFocusedFileProperty() {
     }
 
     public void setLastFocusedFile(Path lastFocusedFile) {
-        this.lastFocusedFile.set(lastFocusedFile);
+        this.lastFocusedFile.set(toRelative(lastFocusedFile));
     }
 
     public FileHistory getFileHistory() {
         return fileHistory;
     }
+
+    private Path toRelative(Path absolutePath) {
+        if (absolutePath == null) {
+            return null;
+        }
+        Path workingDir = Path.of("").toAbsolutePath();
+        try {
+            return workingDir.relativize(absolutePath);
+        } catch (Exception e) {
+            return absolutePath; // fallback
+        }
+    }
+
+    private Path toAbsolute(Path storedPath) {
+        if (storedPath == null) {
+            return null;
+        }
+        Path workingDir = Path.of("").toAbsolutePath();
+        if (!storedPath.isAbsolute()) {
+            return workingDir.resolve(storedPath).normalize();
+        }
+        return storedPath;
+    }
 }
diff --git a/jablib/src/main/java/org/jabref/logic/util/io/FileHistory.java b/jablib/src/main/java/org/jabref/logic/util/io/FileHistory.java
index 7ccbcadc88d..d80e13e1701 100644
--- a/jablib/src/main/java/org/jabref/logic/util/io/FileHistory.java
+++ b/jablib/src/main/java/org/jabref/logic/util/io/FileHistory.java
@@ -27,7 +27,7 @@ public int size() {
 
     @Override
     protected void doAdd(int index, Path element) {
-        history.add(index, element);
+        history.add(index, toRelative(element.toAbsolutePath()));
     }
 
     @Override
@@ -41,11 +41,13 @@ protected Path doRemove(int index) {
     }
 
     /**
-     * Adds the file to the top of the list. If it already is in the list, it is merely moved to the top.
+     * Adds the file to the top of the list. If it already is in the list, it is
+     * merely moved to the top.
      */
     public void newFile(Path file) {
         removeItem(file);
-        this.addFirst(file);
+        this.addFirst(toRelative(file.toAbsolutePath()));
+
         while (size() > HISTORY_SIZE) {
             history.remove(HISTORY_SIZE);
         }
@@ -58,4 +60,21 @@ public void removeItem(Path file) {
     public static FileHistory of(List<Path> list) {
         return new FileHistory(new ArrayList<>(list));
     }
+
+    private Path toRelative(Path absolutePath) {
+        Path workingDir = Path.of("").toAbsolutePath();
+        try {
+            return workingDir.relativize(absolutePath);
+        } catch (Exception e) {
+            return absolutePath; // fallback
+        }
+    }
+
+    private Path toAbsolute(Path storedPath) {
+        Path workingDir = Path.of("").toAbsolutePath();
+        if (!storedPath.isAbsolute()) {
+            return workingDir.resolve(storedPath).normalize();
+        }
+        return storedPath;
+    }
 }