diff --git a/actions/upgrades b/actions/upgrades
index 61bdba698..db808a51f 100755
--- a/actions/upgrades
+++ b/actions/upgrades
@@ -21,6 +21,7 @@ Configures or runs unattended-upgrades
 
 import argparse
 import os
+import pathlib
 import re
 import subprocess
 import sys
@@ -170,46 +171,10 @@ def _check_and_backports_sources():
 
 def _add_apt_preferences():
     """Setup APT preferences to upgrade selected packages from backports."""
-    preferences_path = '/etc/apt/preferences.d'
-    old_preferences_files = map(
-        lambda pref_file: os.path.join(preferences_path, pref_file),
-        ['50freedombox.pref', '50freedombox2.pref'])
-
-    for pref_file in old_preferences_files:
-        os.path.exists(pref_file) and os.remove(pref_file)
-
-    preferences_file = '/etc/apt/preferences.d/50freedombox3.pref'
-    if os.path.exists(preferences_file):
-        print('Preferences up-to-date. Skipping update')
-        return
-
-    warning = 'Explanation: This file is managed by FreedomBox, do not edit.'
-
-    freedombox_preference = '''
-Explanation: Allow carefully selected updates to 'freedombox' from backports.
-Package: freedombox
-Pin: release a=buster-backports
-Pin-Priority: 500
-'''
-
-    matrix_synapse_preferences = '''
-Explanation: Allow carefully selected updates to 'matrix-synapse' from backports.
-Package: matrix-synapse
-Pin: version 1.2*
-Pin-Priority: 500
-
-Explanation: Allow carefully selected updates to 'python3-service-identity' from backports.
-Package: python3-service-identity
-Pin: version 18.1*
-Pin-Priority: 500
-'''
-
-    preferences = "".join(
-        [warning, freedombox_preference, matrix_synapse_preferences])
-
-    print('Updating APT preferences.')
-    with open(preferences_file, 'w') as file_handle:
-        file_handle.write(preferences)
+    for file_name in ['50freedombox.pref', '50freedombox2.pref']:
+        full_path = pathlib.Path('/etc/apt/preferences.d') / file_name
+        if full_path.exists():
+            full_path.unlink()
 
 
 def subcommand_setup_repositories(_):
diff --git a/plinth/modules/upgrades/data/etc/apt/preferences.d/50freedombox3.pref b/plinth/modules/upgrades/data/etc/apt/preferences.d/50freedombox3.pref
new file mode 100644
index 000000000..b4a19265b
--- /dev/null
+++ b/plinth/modules/upgrades/data/etc/apt/preferences.d/50freedombox3.pref
@@ -0,0 +1,16 @@
+Explanation: This file is managed by FreedomBox, do not edit.
+Explanation: Allow carefully selected updates to 'freedombox' from backports.
+Package: freedombox
+Pin: release a=buster-backports
+Pin-Priority: 500
+
+Explanation: matrix-synapse 0.99.5 introduces room version 4. Older version
+Explanation: 0.99.2 in buster won't be able join newly created rooms.
+Package: matrix-synapse
+Pin: release a=buster-backports
+Pin-Priority: 500
+
+Explanation: matrix-synapse >= 1.2 requires python3-service-identity >= 18.1
+Package: python3-service-identity
+Pin: release a=buster-backports
+Pin-Priority: 500