diff --git a/setup/owncloud.sh b/setup/owncloud.sh
index 8f15d03..ad81693 100755
--- a/setup/owncloud.sh
+++ b/setup/owncloud.sh
@@ -31,6 +31,7 @@ if [ ! -f $STORAGE_ROOT/owncloud/config.php ] \
 fi
 
 # Check if ownCloud dir exist, and check if version matches owncloud_ver (if either doesn't - install/upgrade)
+DID_OWNCLOUD_UPGRADE=0
 if [ ! -d /usr/local/lib/owncloud/ ] \
 	|| ! grep -q $owncloud_ver /usr/local/lib/owncloud/version.php; then
 
@@ -66,8 +67,9 @@ if [ ! -d /usr/local/lib/owncloud/ ] \
 	# that error.
 	chown -f -R www-data.www-data $STORAGE_ROOT/owncloud /usr/local/lib/owncloud
 
-	# Run the upgrade script (if ownCloud is already up-to-date it wont matter).
+	# Run the upgrade script.
 	hide_output sudo -u www-data php /usr/local/lib/owncloud/occ upgrade
+	DID_OWNCLOUD_UPGRADE=1
 fi
 
 # ### Configuring ownCloud
@@ -156,6 +158,13 @@ hide_output sudo -u www-data php /usr/local/lib/owncloud/console.php app:enable
 hide_output sudo -u www-data php /usr/local/lib/owncloud/console.php app:enable contacts
 hide_output sudo -u www-data php /usr/local/lib/owncloud/console.php app:enable calendar
 
+if [ $DID_OWNCLOUD_UPGRADE -gt 0 ]; then
+	# When upgrading, run the upgrade script again now that apps are enabled. It seems like
+	# the first upgrade at the top won't work because apps may be disabled during upgrade?
+	# This command will fail if there's nothing to upgrade.
+	hide_output sudo -u www-data php /usr/local/lib/owncloud/occ upgrade
+fi
+
 # Set PHP FPM values to support large file uploads
 # (semicolon is the comment character in this file, hashes produce deprecation warnings)
 tools/editconf.py /etc/php5/fpm/php.ini -c ';' \