How to Back Up an Ubuntu Server to an External Drive, Step by Step

Oct 05, 2025

Backups are like umbrellas: boring until the sky opens. If you've ever run a "quick update", watched the screen go quiet, then felt your stomach drop, this guide is for you. We'll set up snapshots that behave like an undo button for your server, with zero faff and no scary tooling.

What you'll build

A tidy snapshot script that grabs your OS configs, users, app bits, and helper files
Dated restore points you can browse like save games
A "latest" pointer that works on exFAT, plus a nightly schedule and monthly clean-up

Why this rocks

Human-readable, no black-box backups
Fast to test, easy to restore single files or the whole lot
Works with a plain external drive, no vendor ties

Who this helps

Anyone who likes sleep, hates data loss, and wants a backup that is simple, predictable, and repeatable.

Promise

Clear steps, copy-paste commands (delete the placeholders), no machine-specific details. By the end you'll have a calm, boring backup routine, which is exactly what you want from backups.

What to change for your environment

Replace <BACKUP_LABEL> with your chosen neutral label
Replace <HOST_TAG> with a neutral host tag, for example host
If your desktop auto-mounts under /media/$USER/<BACKUP_LABEL>, adjust paths in the helper

01. What you get

A script that archives key system paths into a compressed snapshot
A dated folder per run for multiple restore points
A LATEST.txt pointer when symlinks are not supported
A nightly cron job at 02:15 local time
Monthly pruning on the 1st, default keep ≈35 days
Simple commands for single-file restore and full restore

02. Prerequisites

Ubuntu 22.04 or 24.04 server with sudo
External drive mounted or mountable, any filesystem, exFAT works
Packages: zstd, rsync (usually installed)

sudo apt-get update
sudo apt-get install -y zstd

03. Pick your placeholders

Choose names that do not reveal your environment.

<BACKUP_LABEL>     the drive label, example: BackupDrive
<HOST_TAG>         a short tag for the machine, example: host

If your drive is exFAT and unlabelled, label it once, replace sdX1 with your device:

sudo apt-get install -y exfatprogs
sudo umount /dev/sdX1
sudo exfatlabel /dev/sdX1 <BACKUP_LABEL>

Mount by label when needed:

sudo mkdir -p /mnt/<BACKUP_LABEL>
sudo mount /dev/disk/by-label/<BACKUP_LABEL> /mnt/<BACKUP_LABEL>

04. Install the snapshot script

This script detects the drive by label, creates the folder tree if missing, writes a timestamped snapshot, saves helper files, writes LATEST.txt when symlinks fail, and prunes monthly.

sudo tee /usr/local/sbin/system-snapshot.sh >/dev/null <<'EOF'
#!/usr/bin/env bash
set -euo pipefail

# ===== Settings, change to your placeholders =====
LABEL="${LABEL:-<BACKUP_LABEL>}"      # drive label
HOST_TAG="${HOST_TAG:-<HOST_TAG>}"    # host tag used in the backup path
RETAIN_DAYS="${RETAIN_DAYS:-35}"      # keep ≈1 month
FREE_GIB_MIN="${FREE_GIB_MIN:-5}"     # require at least this much free space

INCLUDE_DIRS=(/etc /root /usr/local /opt /home)

# ===== Resolve & mount the backup drive by label =====
LABEL_MOUNT="/mnt/${LABEL}"
if ! findmnt -rno TARGET -S LABEL="${LABEL}" >/dev/null 2>&1; then
  sudo mkdir -p "${LABEL_MOUNT}"
  sudo mount "/dev/disk/by-label/${LABEL}" "${LABEL_MOUNT}"
fi
DRIVE="$(findmnt -rno TARGET -S LABEL=${LABEL})"
[ -n "${DRIVE}" ] || { echo "Backup drive with label ${LABEL} not mounted"; exit 1; }

# ===== Ensure free space =====
FREE_KB=$(df -Pk "${DRIVE}" | awk 'NR==2{print $4}')
if [ "${FREE_KB:-0}" -lt $((FREE_GIB_MIN*1024*1024)) ]; then
  echo "Not enough free space on ${DRIVE}. Need >= ${FREE_GIB_MIN} GiB. Skipping."
  exit 0
fi

# ===== Paths =====
SNAPS_DIR="${DRIVE}/backups/${HOST_TAG}/snapshots"
TS="$(date +%F_%H%M)"
DEST="${SNAPS_DIR}/${TS}"
LOG="/var/log/system-snapshot.log"

sudo mkdir -p "${DEST}"

# ===== Create archive =====
# Preserve owners, perms, xattrs, ACLs. Exclude volatile paths & the backup drive itself.
sudo tar --zstd -cpf "${DEST}/system.tar.zst" \
  --numeric-owner --xattrs --acls --one-file-system \
  --exclude=/proc --exclude=/sys --exclude=/dev --exclude=/run \
  --exclude=/tmp --exclude=/var/tmp --exclude=/var/cache/apt/archives \
  --exclude="${DRIVE}" \
  "${INCLUDE_DIRS[@]}"

# Quick integrity check
zstd -t "${DEST}/system.tar.zst"

# ===== Helpers =====
dpkg --get-selections | sudo tee "${DEST}/_package_list.txt" >/dev/null || true
sudo crontab -l | sudo tee "${DEST}/_crontab_root.txt" >/dev/null || true
sudo cp -a /etc/fstab "${DEST}/fstab" 2>/dev/null || true
sudo cp -a /etc/apt/sources.list "${DEST}/sources.list" 2>/dev/null || true

# ===== Latest pointer: try symlink, else LATEST.txt for exFAT =====
if ln -sfn "${DEST}" "${SNAPS_DIR}/latest" 2>/dev/null; then
  echo "Updated latest symlink"
else
  echo "${DEST}" | sudo tee "${SNAPS_DIR}/LATEST.txt" >/dev/null
  echo "Wrote latest pointer: ${SNAPS_DIR}/LATEST.txt"
fi

# ===== Monthly prune on day 01, older than RETAIN_DAYS =====
if [ "$(date +%d)" = "01" ]; then
  find "${SNAPS_DIR}" -maxdepth 1 -type d -name "20*" -mtime +"${RETAIN_DAYS}" -print -exec rm -rf {} \;
  echo "Pruned snapshots older than ${RETAIN_DAYS} days"
else
  echo "Skipping prune, not month start"
fi

# ===== README with restore notes =====
sudo tee "${DEST}/RESTORE_README.txt" >/dev/null <<EOF2
Restore checklist:

1) Reinstall Ubuntu & boot.
2) Mount the backup drive:
   sudo mkdir -p /mnt/${LABEL}
   sudo mount /dev/disk/by-label/${LABEL} /mnt/${LABEL}
3) Choose a snapshot:
   SNAP="/mnt/${LABEL}/backups/${HOST_TAG}/snapshots/${TS}"
4) Full extract:
   sudo tar -xpf "\$SNAP/system.tar.zst" -C / --numeric-owner --xattrs --acls
5) Reinstall packages:
   sudo apt-get update
   sudo dpkg --set-selections < "\$SNAP/_package_list.txt"
   sudo apt-get -y dselect-upgrade
EOF2

echo "Snapshot complete at: ${DEST}"
EOF

sudo chmod +x /usr/local/sbin/system-snapshot.sh

05. Create a simple helper to get the latest snapshot

sudo tee /usr/local/bin/snapshot-latest >/dev/null <<'EOF'
#!/usr/bin/env bash
set -euo pipefail
d="/media/<BACKUP_LABEL>/backups/<HOST_TAG>/snapshots"
if [ -L "$d/latest" ]; then
  readlink -f "$d/latest"
elif [ -f "$d/LATEST.txt" ]; then
  cat "$d/LATEST.txt"
else
  ls -1 "$d" | grep -E '^[0-9]{4}-' | sort | tail -1 | sed "s|^|$d/|"
fi
EOF
sudo chmod +x /usr/local/bin/snapshot-latest

Tip: if your system auto-mounts the drive under /media/$USER/<BACKUP_LABEL>, adjust the d=... path accordingly.

06. Run a first snapshot and verify

# optional: set timezone to local
# sudo timedatectl set-timezone Europe/London

sudo /usr/local/sbin/system-snapshot.sh

# Show newest snapshot path
SNAP="$(snapshot-latest)"; echo "$SNAP"

# Peek inside the archive
tar -tf "$SNAP/system.tar.zst" | head

# Verify archive integrity
zstd -t "$SNAP/system.tar.zst" && echo "Archive OK"

07. Schedule nightly at 02:15

# create a log file owned by root
sudo install -o root -g root -m 644 /dev/null /var/log/system-snapshot.log

# add cron line for root
sudo crontab -e
# paste this line, then save
15 2 * * * /usr/local/sbin/system-snapshot.sh >> /var/log/system-snapshot.log 2>&1

# ensure cron is enabled & running
sudo systemctl enable --now cron
sudo systemctl status cron

Check logs:

sudo tail -n 50 /var/log/system-snapshot.log

08. Restore: two common cases

A) Restore a single file from the latest snapshot

SNAP="$(snapshot-latest)"
sudo tar -xpf "$SNAP/system.tar.zst" -C / etc/ssh/sshd_config --numeric-owner --xattrs --acls

B) Full system restore after a clean install

# 1. Mount the backup drive
sudo mkdir -p /mnt/<BACKUP_LABEL>
sudo mount /dev/disk/by-label/<BACKUP_LABEL> /mnt/<BACKUP_LABEL>

# 2. Pick a snapshot
SNAP="$(/usr/local/bin/snapshot-latest | sed "s|^/media/<BACKUP_LABEL>|/mnt/<BACKUP_LABEL>|")"

# 3. Extract to root
sudo tar -xpf "$SNAP/system.tar.zst" -C / --numeric-owner --xattrs --acls

# 4. Reinstall packages
sudo apt-get update
sudo dpkg --set-selections < "$SNAP/_package_list.txt"
sudo apt-get -y dselect-upgrade

# 5. Reboot when ready
sudo reboot

09. Optional additions

Prefer a specific device by UUID

Useful if two drives share a label and might be connected at the same time.

sudo blkid | grep <BACKUP_LABEL>

Then mount by UUID in /etc/fstab:

UUID=<PUT-UUID-HERE>  /mnt/<BACKUP_LABEL>  exfat  uid=1000,gid=1000,defaults  0  0

Adjust the script's mount section to mount /mnt/<BACKUP_LABEL> directly if you use fstab.

Exclude container or VM data

Add these to the tar excludes in the script if relevant:

--exclude=/var/lib/docker --exclude=/var/lib/containers --exclude=/var/lib/libvirt/images

Database dumps

Place before the tar command in the script, or write them into ${DEST} after.

# MariaDB or MySQL
sudo mysqldump --single-transaction --all-databases | zstd > "${DEST}/mysql_all.sql.zst" || true
# PostgreSQL
sudo -u postgres pg_dumpall | zstd > "${DEST}/pg_all.sql.zst" || true

10. Troubleshooting

Permission denied when appending to log: redirection happens before sudo. Use sudo bash -c '... >> /var/log/system-snapshot.log 2>&1' or let cron write it.
Cannot create symlink on the backup drive: exFAT does not support Unix symlinks. The script writes LATEST.txt instead. Use snapshot-latest to resolve the newest snapshot.
No space left: raise FREE_GIB_MIN or prune snapshots.

Manual prune, example:

SNAPS_DIR="/media/<BACKUP_LABEL>/backups/<HOST_TAG>/snapshots"
find "$SNAPS_DIR" -maxdepth 1 -type d -name "20*" -mtime +35 -print -exec rm -rf {} \;

That's it. You now have automated, date-stamped Ubuntu system snapshots to an external drive, with clean restore steps.

@JamieBykovBrett

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