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) {