What are we building?

By the end, your Debian 13 automatically pulls security updates daily and installs them without your involvement. You decide whether and when the server reboots for necessary kernel updates, and you know how to verify that the automation really kicks in. What gets automated are security updates and the conservative stable point releases; larger upgrades of your other software stay deliberately in your hands.

Prerequisites

• A hardened server with an active firewall

Step by step

Step 1: Install the package

sudo apt update
sudo apt install -y unattended-upgrades apt-listchanges

apt-listchanges shows the changelogs on updates – useful if you later do check manually what changed.

Step 2: Enable the automation

The simplest way to switch on the daily run:

sudo dpkg-reconfigure -plow unattended-upgrades

Choose Yes in the dialog. That creates the file /etc/apt/apt.conf.d/20auto-upgrades with this content:

APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Unattended-Upgrade "1";

The 1 means “daily”: update package lists and run unattended upgrades. It’s triggered via the systemd timers apt-daily.timer (package lists) and apt-daily-upgrade.timer (upgrade run) – no separate cron job needed.

Step 3: Define what gets updated

Take a look at /etc/apt/apt.conf.d/50unattended-upgrades:

sudo nano /etc/apt/apt.conf.d/50unattended-upgrades

On Debian 13, three sources are active in the Origins-Pattern block by default:

Unattended-Upgrade::Origins-Pattern {
  "origin=Debian,codename=${distro_codename},label=Debian";
  "origin=Debian,codename=${distro_codename},label=Debian-Security";
  "origin=Debian,codename=${distro_codename}-security,label=Debian-Security";
};

The two Debian-Security lines ensure timely security updates – the actual purpose. The first line (label=Debian) covers the conservative stable updates that only arrive with Debian point releases; so it’s not a risky rolling update, but well-seasoned. If you really want only security updates, comment out the first line with //.

Two options are worth setting explicitly here. Clean up old kernels/packages automatically, otherwise /boot eventually fills up (Remove-Unused-Kernel-Packages is already the default in code, but only appears commented out in the file – set explicitly, the decision is documented):

Unattended-Upgrade::Remove-Unused-Kernel-Packages "true";
Unattended-Upgrade::Remove-Unused-Dependencies "true";

And the most important point – the automatic reboot:

Unattended-Upgrade::Automatic-Reboot "true";
Unattended-Upgrade::Automatic-Reboot-Time "04:00";

For the automatic reboot to be able to trigger on Debian at all, one building block is still missing: unattended-upgrades only reboots if the marker file /var/run/reboot-required exists – and Debian 13 does not create it on kernel updates by default (the responsible hook comes from an Ubuntu helper package that doesn’t exist in Debian; only individual packages like dbus set the file themselves). A two-liner closes the gap:

sudo tee /etc/kernel/postinst.d/zz-reboot-required > /dev/null <<'EOF'
#!/bin/sh
touch /var/run/reboot-required
EOF
sudo chmod +x /etc/kernel/postinst.d/zz-reboot-required

The hook runs after every kernel installation and sets the marker file. From now on, both Automatic-Reboot and the manual check of /var/run/reboot-required work reliably – without the hook, the automatic reboot would simply never trigger on kernel updates.

Step 4: Do a dry run

Test what unattended-upgrades would do, without a real installation:

sudo unattended-upgrade --dry-run --debug

In the debug output, this line is decisive (on a fresh Debian 13, shortened):

Allowed origins are: origin=Debian,codename=trixie,label=Debian, origin=Debian,codename=trixie,label=Debian-Security, origin=Debian,codename=trixie-security,label=Debian-Security
[...]
No packages found that can be upgraded unattended and no pending auto-removals

The Debian-Security sources must appear there. If something is listed, the configuration applies; if the run finds nothing to do (as above), there’s simply no security update pending right now.

When things go wrong

Maintenance & backups

• Still check anyway: automation doesn’t replace attention. Take a monthly look at the log /var/log/unattended-upgrades/unattended-upgrades.log and occasionally run sudo apt update && sudo apt upgrade for the non-security-critical updates.
• Plan for reboots: if you use automatic reboots, make sure your services survive a reboot cleanly (restart: unless-stopped in Docker Compose if you run containers).
• No dedicated backup needed, but note whether you enabled automatic reboots – it later explains why the server was briefly gone at night.