diff --git a/arduino-core/src/processing/app/PreferencesData.java b/arduino-core/src/processing/app/PreferencesData.java
index 6757e7e6e49..0517d96cea4 100644
--- a/arduino-core/src/processing/app/PreferencesData.java
+++ b/arduino-core/src/processing/app/PreferencesData.java
@@ -120,7 +120,7 @@ static protected void save() {
       String[] keys = prefs.keySet().toArray(new String[0]);
       Arrays.sort(keys);
       for (String key : keys) {
-        if (key.startsWith("runtime."))
+        if (key.startsWith("runtime.") || key.startsWith("build_properties_custom."))
           continue;
         writer.println(key + "=" + prefs.get(key));
       }