diff --git a/CHANGELOG.md b/CHANGELOG.md
index 861471f2d69..df600969dad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- We fixed the checkbox in merge dialog "Treat duplicates the same way". Now it works
+
 ### Removed
 
 ## [6.0-alpha.3] – 2025-10-30
diff --git a/jabgui/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java b/jabgui/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java
index 73ea29d6f7e..cc0ad45bef1 100644
--- a/jabgui/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java
+++ b/jabgui/src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java
@@ -57,6 +57,9 @@ public class DuplicateSearch extends SimpleCommand {
     private final BibEntryTypesManager entryTypesManager;
     private final TaskExecutor taskExecutor;
 
+    // For "apply to all entries" functionality.
+    private DuplicateResolverResult rememberedDecision = null;
+
     public DuplicateSearch(Supplier<LibraryTab> tabSupplier,
                            DialogService dialogService,
                            StateManager stateManager,
@@ -83,6 +86,7 @@ public void execute() {
         libraryAnalyzed.set(false);
         autoRemoveExactDuplicates.set(false);
         duplicateCount.set(0);
+        rememberedDecision = null;
 
         if (entries.size() < 2) {
             return;
@@ -160,9 +164,23 @@ private void askResolveStrategy(DuplicateSearchResult result, BibEntry first, Bi
 
         dialog.titleProperty().bind(Bindings.concat(dialog.getTitle()).concat(" (").concat(duplicateProgress.getValue()).concat("/").concat(duplicateTotal).concat(")"));
 
-        DuplicateResolverResult resolverResult = dialogService.showCustomDialogAndWait(dialog)
-                                                              .orElse(DuplicateResolverResult.BREAK);
+        DuplicateResolverResult resolverResult;
+
+        if (preferences.getMergeDialogPreferences().shouldMergeApplyToAllEntries() && rememberedDecision != null) {
+            resolverResult = rememberedDecision;
+        } else {
+            resolverResult = dialogService.showCustomDialogAndWait(dialog)
+                                          .orElse(DuplicateResolverResult.BREAK);
+
+            if (preferences.getMergeDialogPreferences().shouldMergeApplyToAllEntries()) {
+                rememberedDecision = resolverResult;
+            }
+        }
+
+        applyDecisionToResult(result, first, second, resolverResult, dialog);
+    }
 
+    private void applyDecisionToResult(DuplicateSearchResult result, BibEntry first, BibEntry second, DuplicateResolverResult resolverResult, DuplicateResolverDialog dialog) {
         if ((resolverResult == DuplicateResolverResult.KEEP_LEFT)
                 || (resolverResult == DuplicateResolverResult.AUTOREMOVE_EXACT)) {
             result.remove(second);