diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3529222a37f..329bc243c07 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the command line export using `--exportMatches` flag does not create an output bib file [#9581](https://github.com/JabRef/jabref/issues/9581)
 - We fixed an issue where custom field in the custom entry types could not be set to mulitline [#9609](https://github.com/JabRef/jabref/issues/9609)
 - We fixed an issue where the Office XML exporter did not resolve BibTeX-Strings when exporting entries [forum#3741](https://discourse.jabref.org/t/exporting-bibtex-constant-strings-to-ms-office-2007-xml/3741)
+- We fixed an issue where the Merge Entries Toolbar configuration was not saved after hitting 'Merge Entries' button [#9091](https://github.com/JabRef/jabref/issues/9091)
 - We fixed an issue where the password is saved locally if user wants to use proxy with authentication [#8055](https://github.com/JabRef/jabref/issues/8055)
 - JabRef is now more relaxed when parsing field content: In case a field content ended with `\`, the combination `\}` was treated as plain `}`. [#9668](https://github.com/JabRef/jabref/issues/9668)
 - We resolved an issue that cut off the number of group entries when it exceedet four digits. [#8797](https://github.com/JabRef/jabref/issues/8797)
diff --git a/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java
index 205e4df75de..15a27d4f810 100644
--- a/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java
+++ b/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java
@@ -122,6 +122,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
         this.setResultConverter(button -> {
             // Updates the window state on button press
             stateManager.setDialogWindowState(getClass().getSimpleName(), new DialogWindowState(this.getX(), this.getY(), this.getDialogPane().getHeight(), this.getDialogPane().getWidth()));
+            threeWayMerge.saveConfiguration();
 
             if (button.equals(first)) {
                 return DuplicateResolverResult.KEEP_LEFT;
diff --git a/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java b/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java
index 23a82a1ddde..8be99e1bfee 100644
--- a/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java
+++ b/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java
@@ -36,6 +36,7 @@ private void init() {
         ButtonType replaceEntries = new ButtonType(Localization.lang("Merge entries"), ButtonBar.ButtonData.OK_DONE);
         this.getDialogPane().getButtonTypes().setAll(ButtonType.CANCEL, replaceEntries);
         this.setResultConverter(buttonType -> {
+            threeWayMergeView.saveConfiguration();
             if (buttonType.equals(replaceEntries)) {
                 return new EntriesMergeResult(one, two, threeWayMergeView.getLeftEntry(), threeWayMergeView.getRightEntry(), threeWayMergeView.getMergedEntry());
             } else {
diff --git a/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java b/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java
index 5767d747a4c..fd2b1b3105f 100644
--- a/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java
+++ b/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java
@@ -191,4 +191,8 @@ public BibEntry getLeftEntry() {
     public BibEntry getRightEntry() {
         return viewModel.getRightEntry();
     }
+
+    public void saveConfiguration() {
+        toolbar.saveToolbarConfiguration();
+    }
 }
diff --git a/src/main/java/org/jabref/gui/mergeentries/newmergedialog/toolbar/ThreeWayMergeToolbar.java b/src/main/java/org/jabref/gui/mergeentries/newmergedialog/toolbar/ThreeWayMergeToolbar.java
index 8a656830e4d..03a595741e5 100644
--- a/src/main/java/org/jabref/gui/mergeentries/newmergedialog/toolbar/ThreeWayMergeToolbar.java
+++ b/src/main/java/org/jabref/gui/mergeentries/newmergedialog/toolbar/ThreeWayMergeToolbar.java
@@ -17,9 +17,11 @@
 import org.jabref.gui.mergeentries.newmergedialog.DiffMethod;
 import org.jabref.gui.mergeentries.newmergedialog.diffhighlighter.DiffHighlighter.BasicDiffMethod;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.preferences.GuiPreferences;
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.views.ViewLoader;
+import com.google.common.base.Enums;
 import com.tobiasdiez.easybind.EasyBind;
 import com.tobiasdiez.easybind.EasyBinding;
 import jakarta.inject.Inject;
@@ -66,7 +68,7 @@ public ThreeWayMergeToolbar() {
     public void initialize() {
         showDiff = EasyBind.map(plainTextOrDiffComboBox.valueProperty(), plainTextOrDiff -> plainTextOrDiff == PlainTextOrDiff.Diff);
         plainTextOrDiffComboBox.getItems().addAll(PlainTextOrDiff.values());
-        plainTextOrDiffComboBox.getSelectionModel().select(PlainTextOrDiff.Diff);
+
         plainTextOrDiffComboBox.setConverter(new StringConverter<>() {
             @Override
             public String toString(PlainTextOrDiff plainTextOrDiff) {
@@ -81,7 +83,7 @@ public PlainTextOrDiff fromString(String string) {
 
         diffViewComboBox.disableProperty().bind(notShowDiffProperty());
         diffViewComboBox.getItems().addAll(DiffView.values());
-        diffViewComboBox.getSelectionModel().select(DiffView.UNIFIED);
+
         diffViewComboBox.setConverter(new StringConverter<>() {
             @Override
             public String toString(DiffView diffView) {
@@ -105,11 +107,30 @@ public DiffView fromString(String string) {
             }
         }));
 
-        diffHighlightingMethodToggleGroup.selectToggle(highlightWordsRadioButton);
-        plainTextOrDiffComboBox.valueProperty().set(PlainTextOrDiff.Diff);
-
         onlyShowChangedFieldsCheck.selectedProperty().bindBidirectional(preferencesService.getGuiPreferences().mergeShowChangedFieldOnlyProperty());
         onlyShowChangedFields.bind(onlyShowChangedFieldsCheck.selectedProperty());
+
+        loadSavedConfiguration();
+    }
+
+    private void loadSavedConfiguration() {
+        GuiPreferences guiPreferences = preferencesService.getGuiPreferences();
+
+        PlainTextOrDiff plainTextOrDiffPreference = guiPreferences.getMergeShouldShowDiff() ? PlainTextOrDiff.Diff : PlainTextOrDiff.PLAIN_TEXT;
+        plainTextOrDiffComboBox.getSelectionModel().select(plainTextOrDiffPreference);
+
+        DiffView diffViewPreference = guiPreferences.getMergeShouldShowUnifiedDiff() ? DiffView.UNIFIED : DiffView.SPLIT;
+        diffViewComboBox.getSelectionModel().select(diffViewPreference);
+
+        diffHighlightingMethodToggleGroup.selectToggle(guiPreferences.getMergeHighlightWords() ? highlightWordsRadioButton : highlightCharactersRadioButtons);
+    }
+
+    public void saveToolbarConfiguration() {
+        preferencesService.getGuiPreferences().setMergeShouldShowDiff(plainTextOrDiffComboBox.getValue() == PlainTextOrDiff.Diff);
+        preferencesService.getGuiPreferences().setMergeShouldShowUnifiedDiff(diffViewComboBox.getValue() == DiffView.UNIFIED);
+
+        boolean highlightWordsRadioButtonValue = diffHighlightingMethodToggleGroup.getSelectedToggle().equals(highlightWordsRadioButton);
+        preferencesService.getGuiPreferences().setMergeHighlightWords(highlightWordsRadioButtonValue);
     }
 
     public ObjectProperty<DiffView> diffViewProperty() {
@@ -185,6 +206,10 @@ public enum PlainTextOrDiff {
             this.value = value;
         }
 
+        public static PlainTextOrDiff parse(String name) {
+            return Enums.getIfPresent(PlainTextOrDiff.class, name).or(Diff);
+        }
+
         public String getValue() {
             return value;
         }
@@ -203,6 +228,10 @@ public enum DiffView {
             this.value = value;
         }
 
+        public static DiffView parse(String name) {
+            return Enums.getIfPresent(DiffView.class, name).or(UNIFIED);
+        }
+
         public String getValue() {
             return value;
         }
diff --git a/src/main/java/org/jabref/preferences/GuiPreferences.java b/src/main/java/org/jabref/preferences/GuiPreferences.java
index fc0bd899286..c868ba3d751 100644
--- a/src/main/java/org/jabref/preferences/GuiPreferences.java
+++ b/src/main/java/org/jabref/preferences/GuiPreferences.java
@@ -33,6 +33,9 @@ public class GuiPreferences {
 
     private final StringProperty lastSelectedIdBasedFetcher;
     private final ObjectProperty<DiffMode> mergeDiffMode;
+    private final BooleanProperty mergeShouldShowDiff;
+    private final BooleanProperty mergeShouldShowUnifiedDiff;
+    private final BooleanProperty mergeHighlightWords;
     private final BooleanProperty mergeShowChangedFieldsOnly;
     private final DoubleProperty sidePaneWidth;
 
@@ -46,6 +49,9 @@ public GuiPreferences(double positionX,
                           FileHistory fileHistory,
                           String lastSelectedIdBasedFetcher,
                           DiffMode mergeDiffMode,
+                          boolean mergeShouldShowDiff,
+                          boolean mergeShouldShowUnifiedDiff,
+                          boolean mergeHighlightWords,
                           double sidePaneWidth,
                           boolean mergeShowChangedFieldsOnly) {
         this.positionX = new SimpleDoubleProperty(positionX);
@@ -57,6 +63,10 @@ public GuiPreferences(double positionX,
         this.lastFocusedFile = new SimpleObjectProperty<>(lastFocusedFile);
         this.lastSelectedIdBasedFetcher = new SimpleStringProperty(lastSelectedIdBasedFetcher);
         this.mergeDiffMode = new SimpleObjectProperty<>(mergeDiffMode);
+        this.mergeShouldShowDiff = new SimpleBooleanProperty(mergeShouldShowDiff);
+        this.mergeShouldShowUnifiedDiff = new SimpleBooleanProperty(mergeShouldShowUnifiedDiff);
+        this.mergeHighlightWords = new SimpleBooleanProperty(mergeHighlightWords);
+
         this.sidePaneWidth = new SimpleDoubleProperty(sidePaneWidth);
         this.fileHistory = fileHistory;
         this.mergeShowChangedFieldsOnly = new SimpleBooleanProperty(mergeShowChangedFieldsOnly);
@@ -170,6 +180,42 @@ public void setMergeDiffMode(DiffMode mergeDiffMode) {
         this.mergeDiffMode.set(mergeDiffMode);
     }
 
+    public boolean getMergeShouldShowDiff() {
+        return mergeShouldShowDiff.get();
+    }
+
+    public BooleanProperty mergeShouldShowDiffProperty() {
+        return mergeShouldShowDiff;
+    }
+
+    public void setMergeShouldShowDiff(boolean mergeShouldShowDiff) {
+        this.mergeShouldShowDiff.set(mergeShouldShowDiff);
+    }
+
+    public boolean getMergeShouldShowUnifiedDiff() {
+        return mergeShouldShowUnifiedDiff.get();
+    }
+
+    public BooleanProperty mergeShouldShowUnifiedDiffProperty() {
+        return mergeShouldShowUnifiedDiff;
+    }
+
+    public void setMergeShouldShowUnifiedDiff(boolean mergeShouldShowUnifiedDiff) {
+        this.mergeShouldShowUnifiedDiff.set(mergeShouldShowUnifiedDiff);
+    }
+
+    public boolean getMergeHighlightWords() {
+        return mergeHighlightWords.get();
+    }
+
+    public BooleanProperty mergeHighlightWordsProperty() {
+        return mergeHighlightWords;
+    }
+
+    public void setMergeHighlightWords(boolean mergeHighlightsWords) {
+        this.mergeHighlightWords.set(mergeHighlightsWords);
+    }
+
     public double getSidePaneWidth() {
         return sidePaneWidth.get();
     }
diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
index f6322a7e529..8db213d76c4 100644
--- a/src/main/java/org/jabref/preferences/JabRefPreferences.java
+++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -238,6 +238,11 @@ public class JabRefPreferences implements PreferencesService {
 
     // merge related
     public static final String MERGE_ENTRIES_DIFF_MODE = "mergeEntriesDiffMode";
+    public static final String MERGE_ENTRIES_SHOULD_SHOW_DIFF = "mergeEntriesShouldShowDiff";
+    public static final String MERGE_ENTRIES_SHOULD_SHOW_UNIFIED_DIFF = "mergeEntriesShouldShowUnifiedDiff";
+    public static final String MERGE_ENTRIES_HIGHLIGHT_WORDS = "mergeEntriesHighlightWords";
+
+
     public static final String MERGE_SHOW_ONLY_CHANGED_FIELDS = "mergeShowOnlyChangedFields";
 
     public static final String CUSTOM_EXPORT_FORMAT = "customExportFormat";
@@ -587,6 +592,9 @@ private JabRefPreferences() {
         defaults.put(DEFAULT_SHOW_SOURCE, Boolean.FALSE);
 
         defaults.put(MERGE_ENTRIES_DIFF_MODE, DiffMode.WORD.name());
+        defaults.put(MERGE_ENTRIES_SHOULD_SHOW_DIFF, Boolean.TRUE);
+        defaults.put(MERGE_ENTRIES_SHOULD_SHOW_UNIFIED_DIFF, Boolean.TRUE);
+        defaults.put(MERGE_ENTRIES_HIGHLIGHT_WORDS, Boolean.TRUE);
         defaults.put(MERGE_SHOW_ONLY_CHANGED_FIELDS, Boolean.FALSE);
 
         defaults.put(SHOW_RECOMMENDATIONS, Boolean.TRUE);
@@ -2510,6 +2518,9 @@ public GuiPreferences getGuiPreferences() {
                 getFileHistory(),
                 get(ID_ENTRY_GENERATOR),
                 DiffMode.parse(get(MERGE_ENTRIES_DIFF_MODE)),
+                getBoolean(MERGE_ENTRIES_SHOULD_SHOW_DIFF),
+                getBoolean(MERGE_ENTRIES_SHOULD_SHOW_UNIFIED_DIFF),
+                getBoolean(MERGE_ENTRIES_HIGHLIGHT_WORDS),
                 getDouble(SIDE_PANE_WIDTH),
                 getBoolean(MERGE_SHOW_ONLY_CHANGED_FIELDS));
 
@@ -2535,6 +2546,9 @@ public GuiPreferences getGuiPreferences() {
         guiPreferences.getFileHistory().addListener((InvalidationListener) change -> storeFileHistory(guiPreferences.getFileHistory()));
         EasyBind.listen(guiPreferences.lastSelectedIdBasedFetcherProperty(), (obs, oldValue, newValue) -> put(ID_ENTRY_GENERATOR, newValue));
         EasyBind.listen(guiPreferences.mergeDiffModeProperty(), (obs, oldValue, newValue) -> put(MERGE_ENTRIES_DIFF_MODE, newValue.name()));
+        EasyBind.listen(guiPreferences.mergeShouldShowDiffProperty(), (obs, oldValue, newValue) -> putBoolean(MERGE_ENTRIES_SHOULD_SHOW_DIFF, newValue));
+        EasyBind.listen(guiPreferences.mergeShouldShowUnifiedDiffProperty(), (obs, oldValue, newValue) -> putBoolean(MERGE_ENTRIES_SHOULD_SHOW_UNIFIED_DIFF, newValue));
+        EasyBind.listen(guiPreferences.mergeHighlightWordsProperty(), (obs, oldValue, newValue) -> putBoolean(MERGE_ENTRIES_HIGHLIGHT_WORDS, newValue));
         EasyBind.listen(guiPreferences.sidePaneWidthProperty(), (obs, oldValue, newValue) -> putDouble(SIDE_PANE_WIDTH, newValue.doubleValue()));
         EasyBind.listen(guiPreferences.mergeShowChangedFieldOnlyProperty(), (obs, oldValue, newValue) -> putBoolean(MERGE_SHOW_ONLY_CHANGED_FIELDS, newValue));
 
diff --git a/src/test/java/org/jabref/logic/citationstyle/CitationStyleTest.java b/src/test/java/org/jabref/logic/citationstyle/CitationStyleTest.java
index b05aed909a5..6bdbac10b98 100644
--- a/src/test/java/org/jabref/logic/citationstyle/CitationStyleTest.java
+++ b/src/test/java/org/jabref/logic/citationstyle/CitationStyleTest.java
@@ -27,10 +27,11 @@ void testDefaultCitation() {
         String citation = CitationStyleGenerator.generateCitation(TestEntry.getTestEntry(), CitationStyle.getDefault().getSource(), CitationStyleOutputFormat.HTML, context, new BibEntryTypesManager());
 
         // if the default citation style changes this has to be modified
-        String expected = "  <div class=\"csl-entry\">\n"
-                          + "    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">B. Smith, B. Jones, and J. Williams, &ldquo;Title of the test entry,&rdquo; <span style=\"font-style: italic\">BibTeX Journal</span>, vol. 34, no. 3, pp. 45&ndash;67, 2016-07, doi: 10.1001/bla.blubb.</div>\n"
-                          + "  </div>\n"
-                          + "";
+        String expected = """
+                  <div class="csl-entry">
+                    <div class="csl-left-margin">[1]</div><div class="csl-right-inline">B. Smith, B. Jones, and J. Williams, &ldquo;Title of the test entry,&rdquo; <span style="font-style: italic">BibTeX Journal</span>, vol. 34, no. 3, pp. 45&ndash;67, Jul. 2016, doi: 10.1001/bla.blubb.</div>
+                  </div>
+                """;
 
         assertEquals(expected, citation);
     }