diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48482f765e9..20f70eff80d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -126,6 +126,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
 - We fixed an issue when click on entry at "Check Integrity" wasn't properly focusing the entry and field. [#11997](https://github.com/JabRef/jabref/issues/11997)
 - We fixed an issue with the ui not scaling when changing the font size [#11219](https://github.com/JabRef/jabref/issues/11219)
+- We fixed an issue where a custom application for external file types would not be saved [#112311](https://github.com/JabRef/jabref/issues/12311)
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/preferences/externalfiletypes/ExternalFileTypesTabViewModel.java b/src/main/java/org/jabref/gui/preferences/externalfiletypes/ExternalFileTypesTabViewModel.java
index a0c4866fc2e..d3c0a8aaf2b 100644
--- a/src/main/java/org/jabref/gui/preferences/externalfiletypes/ExternalFileTypesTabViewModel.java
+++ b/src/main/java/org/jabref/gui/preferences/externalfiletypes/ExternalFileTypesTabViewModel.java
@@ -82,7 +82,12 @@ public boolean edit(ExternalFileTypeItemViewModel type) {
         ExternalFileTypeItemViewModel typeToModify = new ExternalFileTypeItemViewModel(type.toExternalFileType());
         showEditDialog(typeToModify, Localization.lang("Edit file type"));
 
-        if (!isValidExternalFileType(typeToModify)) {
+        if (type.extensionProperty().get().equals(typeToModify.extensionProperty().get())) {
+            if (withEmptyValue(typeToModify)) {
+                LOGGER.warn("One of the fields is empty or invalid. Not saving.");
+                return false;
+            }
+        } else if (!isValidExternalFileType(typeToModify)) {
             return false;
         }
 
@@ -97,12 +102,12 @@ public void remove(ExternalFileTypeItemViewModel type) {
 
     public boolean isValidExternalFileType(ExternalFileTypeItemViewModel item) {
         if (withEmptyValue(item)) {
-            LOGGER.debug("One of the fields is empty or invalid.");
+            LOGGER.warn("One of the fields is empty or invalid. Not saving.");
             return false;
         }
 
         if (!isUniqueExtension(item)) {
-            LOGGER.debug("File Extension exists already.");
+            LOGGER.warn("File Extension already exists. Not saving.");
             return false;
         }