How to Set Up Automated Backups on Ubuntu with rsync and Cron

rsync is the gold standard for Linux backups because it:

• Only transfers changed files (incremental), making subsequent backups fast
• Preserves file permissions, ownership, timestamps, and symbolic links
• Works over SSH for remote backups
• Is pre-installed on virtually every Linux distribution
• Supports compression during transfer to save bandwidth

Combined with cron for scheduling, you get a reliable, zero-cost backup system.

The fundamental rsync backup command:

rsync -avz --delete /home/user/documents/ /mnt/backup/documents/

Flags explained:

• -a (archive) — preserves permissions, timestamps, symlinks, etc.
• -v (verbose) — shows files being transferred
• -z (compress) — compresses data during transfer
• --delete — removes files from backup that were deleted from source

Important: The trailing slash on the source path (documents/) means "copy the contents of this directory." Without it, rsync would create a documents subdirectory inside the destination.

Create a reusable backup script at /usr/local/bin/backup.sh:

#!/bin/bash
set -euo pipefail

# Configuration
SOURCE_DIRS=(
  "/home/user/documents"
  "/home/user/projects"
  "/etc"
)
BACKUP_ROOT="/mnt/backup"
LOG_FILE="/var/log/backup.log"
DATE=$(date +%Y-%m-%d_%H%M)

# Start logging
echo "=== Backup started: $DATE ===" >> "$LOG_FILE"

for dir in "${SOURCE_DIRS[@]}"; do
  dirname=$(basename "$dir")
  dest="$BACKUP_ROOT/$dirname"
  mkdir -p "$dest"

  rsync -az --delete \
    --exclude=".cache" \
    --exclude="node_modules" \
    --exclude=".git" \
    "$dir/" "$dest/" \
    >> "$LOG_FILE" 2>&1

  echo "  Backed up: $dir -> $dest" >> "$LOG_FILE"
done

echo "=== Backup finished: $(date +%Y-%m-%d_%H%M) ===" >> "$LOG_FILE"

Make it executable:

sudo chmod +x /usr/local/bin/backup.sh

To back up to a remote server, use rsync over SSH:

rsync -avz --delete \
  -e "ssh -p 22 -i ~/.ssh/backup_key" \
  /home/user/documents/ \
  backupuser@192.168.1.100:/backups/documents/

Setting up SSH key authentication (so cron can run without a password prompt):

# Generate a dedicated backup key
ssh-keygen -t ed25519 -f ~/.ssh/backup_key -N ""

# Copy it to the remote server
ssh-copy-id -i ~/.ssh/backup_key backupuser@192.168.1.100

# Test the connection
ssh -i ~/.ssh/backup_key backupuser@192.168.1.100 echo "Connected!"

Open the crontab editor:

crontab -e

Add a schedule. Common patterns:

# Daily at 2:00 AM
0 2 * * * /usr/local/bin/backup.sh

# Every 6 hours
0 */6 * * * /usr/local/bin/backup.sh

# Weekdays at 11 PM
0 23 * * 1-5 /usr/local/bin/backup.sh

# Sunday at 3 AM (weekly full backup)
0 3 * * 0 /usr/local/bin/backup.sh

Verify your crontab was saved:

crontab -l

To prevent your backup drive from filling up, add rotation to keep only the last 7 daily backups:

#!/bin/bash
BACKUP_ROOT="/mnt/backup"
DAILY_DIR="$BACKUP_ROOT/daily"
MAX_BACKUPS=7
TODAY=$(date +%Y-%m-%d)
DEST="$DAILY_DIR/$TODAY"

# Create today's backup using hard links from yesterday (saves space)
LATEST=$(ls -1d "$DAILY_DIR"/2* 2>/dev/null | tail -1)
if [ -n "$LATEST" ]; then
  cp -al "$LATEST" "$DEST"
fi

# Sync changes
rsync -az --delete /home/user/documents/ "$DEST/documents/"

# Remove old backups beyond MAX_BACKUPS
ls -1d "$DAILY_DIR"/2* | head -n -$MAX_BACKUPS | xargs rm -rf

echo "Backup complete: $DEST (keeping last $MAX_BACKUPS)"

This approach uses hard links (cp -al) so unchanged files do not consume extra disk space.

How do I restore files from a backup?

Just rsync in the other direction: rsync -avz /mnt/backup/documents/ /home/user/documents/. Or copy individual files with cp.

How much disk space do incremental backups use?

The first backup copies everything. Subsequent backups only transfer changed files, typically using 1-5% of the full backup size.

Can I back up to cloud storage like S3?

rsync does not support S3 directly. Use rclone instead, which has a similar syntax but supports S3, Google Drive, Dropbox, and 40+ cloud providers.

What if a backup fails?

rsync is safe — a failed backup leaves the previous backup intact. Add error handling and email notifications to your script to be alerted of failures.