diff --git a/extensions/pref/autoconfig/test/unit/test_autoconfig_custom_path.js b/extensions/pref/autoconfig/test/unit/test_autoconfig_custom_path.js
--- a/extensions/pref/autoconfig/test/unit/test_autoconfig_custom_path.js
+++ b/extensions/pref/autoconfig/test/unit/test_autoconfig_custom_path.js
@@ -9,10 +9,13 @@
   let testDirName = do_get_cwd().clone();
   Services.env.set("MOZ_SYSTEM_CONFIG_DIR", testDirName.path);
 
   updateAppInfo();
 
+  try {
+    Services.dirsvc.undefine("SysConfD");
+  } catch (e) {}
   let customSysConfD = Services.dirsvc.get("SysConfD", Ci.nsIFile);
   let parent = customSysConfD.parent;
   let child = customSysConfD.leafName;
   notEqual("/etc", parent.path, "SysConfD is not in /etc");
   equal("xpcshell", child, "SysConfD is xpcshell");
diff --git a/extensions/pref/autoconfig/test/unit/test_autoconfig_default_path.js b/extensions/pref/autoconfig/test/unit/test_autoconfig_default_path.js
--- a/extensions/pref/autoconfig/test/unit/test_autoconfig_default_path.js
+++ b/extensions/pref/autoconfig/test/unit/test_autoconfig_default_path.js
@@ -6,8 +6,11 @@
 );
 
 function run_test() {
   updateAppInfo();
 
+  try {
+    Services.dirsvc.undefine("SysConfD");
+  } catch (e) {}
   let defaultSysConfD = Services.dirsvc.get("SysConfD", Ci.nsIFile);
   equal("/etc/xpcshell", defaultSysConfD.path, "SysConfD is in /etc");
 }
diff --git a/modules/libpref/Preferences.cpp b/modules/libpref/Preferences.cpp
--- a/modules/libpref/Preferences.cpp
+++ b/modules/libpref/Preferences.cpp
@@ -4917,27 +4917,10 @@
                            ArrayLength(specialFiles));
   if (NS_FAILED(rv)) {
     NS_WARNING("Error parsing application default preferences.");
   }
 
-#if defined(MOZ_WIDGET_GTK)
-  // Under Flatpak/Snap package, load /etc/firefox/defaults/pref/*.js.
-  if (mozilla::widget::IsRunningUnderFlatpakOrSnap()) {
-    nsCOMPtr<nsIFile> defaultSnapPrefDir;
-    rv = NS_GetSpecialDirectory(NS_OS_SYSTEM_CONFIG_DIR,
-                                getter_AddRefs(defaultSnapPrefDir));
-    NS_ENSURE_SUCCESS(rv, rv);
-    defaultSnapPrefDir->AppendNative("defaults"_ns);
-    defaultSnapPrefDir->AppendNative("pref"_ns);
-
-    rv = pref_LoadPrefsInDir(defaultSnapPrefDir, nullptr, 0);
-    if (NS_FAILED(rv)) {
-      NS_WARNING("Error parsing application default preferences under Snap.");
-    }
-  }
-#endif
-
   // Load jar:$app/omni.jar!/defaults/preferences/*.js
   // or jar:$gre/omni.jar!/defaults/preferences/*.js.
   RefPtr<nsZipArchive> appJarReader = Omnijar::GetReader(Omnijar::APP);
 
   // GetReader(Omnijar::APP) returns null when `$app == $gre`, in
@@ -5006,10 +4989,28 @@
       // Do we care if a file provided by this process fails to load?
       pref_LoadPrefsInDir(path, nullptr, 0);
     }
   }
 
+#if defined(MOZ_WIDGET_GTK)
+  // To ensure the system-wide preferences are not overwritten by
+  // firefox/browser/defauts/preferences/*.js we need to load
+  // the /etc/firefox/defaults/pref/*.js settings as last.
+  // Under Flatpak, the NS_OS_SYSTEM_CONFIG_DIR points to /app/etc/firefox
+  nsCOMPtr<nsIFile> defaultSystemPrefDir;
+  rv = NS_GetSpecialDirectory(NS_OS_SYSTEM_CONFIG_DIR,
+                              getter_AddRefs(defaultSystemPrefDir));
+  NS_ENSURE_SUCCESS(rv, rv);
+  defaultSystemPrefDir->AppendNative("defaults"_ns);
+  defaultSystemPrefDir->AppendNative("pref"_ns);
+
+  rv = pref_LoadPrefsInDir(defaultSystemPrefDir, nullptr, 0);
+  if (NS_FAILED(rv)) {
+    NS_WARNING("Error parsing application default preferences.");
+  }
+#endif
+
   if (XRE_IsParentProcess()) {
     SetupTelemetryPref();
   }
 
   if (aIsStartup) {