Create services & timers
/etc/systemd/user/update-user-flatpaks.service
[Unit]
Description=Update user Flatpaks
[Service]
Type=oneshot
ExecStart=/usr/bin/flatpak update --assumeyes --noninteractive
[Install]
WantedBy=default.target
/etc/systemd/system/update-system-flatpaks.service
[Unit]
Description=Update system Flatpaks
After=network-online.target
Wants=network-online.target
[Service]
Type=oneshot
ExecStart=/usr/bin/flatpak update --assumeyes --noninteractive --system
[Install]
WantedBy=multi-user.target
/etc/systemd/user/update-user-flatpaks.timer
[Unit]
Description=Update user Flatpaks daily
[Timer]
OnCalendar=daily
Persistent=true
[Install]
WantedBy=timers.target
/etc/systemd/system/update-system-flatpaks.timer
[Unit]
Description=Update system Flatpaks daily
[Timer]
OnCalendar=daily
Persistent=true
[Install]
WantedBy=timers.target
Enable timers
systemctl --user enable --now update-user-flatpaks.timer
sudo systemctl --system enable --now update-system-flatpaks.timer