Move MariaDB Data Directory to /home/mysql on Debian (Automated with Shell Script)

If you’re running MariaDB (or MySQL compatible) on a Debian server, by default your database files live under:

/var/lib/mysql

That’s fine until your root disk starts filling up, or you want your databases on a larger or faster volume mounted under /home.

In this guide, we’ll:

Move MariaDB’s data directory from /var/lib/mysql to /home/mysql
Use a POSIX sh shell script that:
- Creates backups automatically
- Handles permissions and systemd hardening
- Adjusts AppArmor if needed
- Rolls back if something goes wrong

You can use this on Debian 12 (and similar) with mariadb.service running under systemd.

Why Move MariaDB to /home/mysql?

Common reasons:

Your / (root) filesystem is small or almost full
You’ve attached a bigger disk and mounted it at /home
You want a clean separation of OS files and data files
You’re planning for better performance and easier backup strategies

Instead of manually fighting with permissions, systemd, and AppArmor every time, we’ll let a script do the heavy lifting.

Prerequisites

Before you start, make sure:

You are on a system using systemd
MariaDB is installed and managed as mariadb.service
You can run commands as root (or via sudo)
rsync is installed:

apt install rsync -y

Important: Always back up your databases before any migration. The script itself creates backups of the data directory, but having your own mariadb-dump is wise.

Example full backup:

mariadb-dump --add-drop-table --all-databases | gzip > /home/alldatabases.sql.gz

What the Script Does

The script:

Verifies you are root and that mariadb.service exists
Stops MariaDB
Backs up the existing data directory /var/lib/mysql
Creates /home/mysql (and backs up its contents if it’s non-empty)
Uses rsync to copy all data from /var/lib/mysql to /home/mysql
Sets correct ownership and permissions
Moves the original /var/lib/mysql aside and replaces it with a symlink to /home/mysql
Creates a systemd override for mariadb.service:
- ProtectHome=read-only
- ReadWritePaths=/home/mysql
Updates AppArmor (if a mysqld profile exists) to allow /home/mysql
Starts MariaDB again
If starting fails, it rolls back:
- Restores the original directory
- Removes the override
- Tries to start MariaDB from the original location

This gives you:

A safer migration
Automatic rollback in case something breaks
Backups kept with timestamps

Step-by-Step: Using the Script

1. Create the Script File

nano /root/move-mariadb-to-home.sh

Paste the full script below (in the next section) into that file, then save and exit.

2. Make the Script Executable

chmod +x /root/move-mariadb-to-home.sh

3. Run the Script

Run it as root:

/root/move-mariadb-to-home.sh

You’ll see logs like:

[*] Stopping MariaDB...
[*] Backing up old data directory /var/lib/mysql to /var/lib/mysql.backup-20251129-171500 ...
[*] Syncing data from /var/lib/mysql to /home/mysql ...
[*] Replacing /var/lib/mysql with symlink to /home/mysql ...
[*] Configuring systemd override at /etc/systemd/system/mariadb.service.d/override.conf ...
[*] Starting MariaDB with new data location...
[*] MariaDB started successfully.

If something fails, the script will attempt a rollback and tell you where the backups are.

Verifying the New Setup

After running the script, verify:

Check MariaDB status

systemctl status mariadb

You should see active (running).

Check directories and symlink

ls -ld /var/lib/mysql
ls -ld /home/mysql

Expected:

/var/lib/mysql is a symlink → /home/mysql
/home/mysql is owned by mysql:mysql

Check datadir value

MariaDB will still report /var/lib/mysql as the data directory:

mysql -e "SHOW VARIABLES LIKE 'datadir';"

Even though it says /var/lib/mysql/, the actual files now live in /home/mysql thanks to the symlink.

Full Script: move-mariadb-to-home.sh

Paste this into /root/move-mariadb-to-home.sh:

#!/bin/sh
#
# Move MariaDB data directory from /var/lib/mysql to /home/mysql on Debian 12
# with backups, fault tolerance, and basic auto-correction.
#
# Must be run as root.

set -eu

OLD_DATADIR="/var/lib/mysql"
NEW_DATADIR="/home/mysql"
BACKUP_SUFFIX="$(date +%Y%m%d-%H%M%S)"

log() {
    echo "[*] $*"
}

err() {
    echo "[!] $*" >&2
}

# --- Safety checks ---------------------------------------------------------

if [ "$(id -u)" != "0" ]; then
    err "This script must be run as root."
    exit 1
fi

if ! command -v systemctl >/dev/null 2>&1; then
    err "systemctl not found. This script is intended for systemd-based systems."
    exit 1
fi

if ! systemctl list-unit-files | grep -q '^mariadb.service'; then
    err "mariadb.service not found. Are you sure MariaDB is installed?"
    exit 1
fi

if [ -L "$OLD_DATADIR" ]; then
    log "$OLD_DATADIR is already a symlink. Aborting to avoid nested moves."
    ls -ld "$OLD_DATADIR"
    exit 1
fi

if [ ! -d "$OLD_DATADIR" ]; then
    err "Old data directory $OLD_DATADIR does not exist or is not a directory."
    exit 1
fi

# --- Stop MariaDB ---------------------------------------------------------

log "Stopping MariaDB..."
if ! systemctl stop mariadb; then
    err "Failed to stop mariadb.service. Aborting."
    exit 1
fi

# --- Prepare target directory ---------------------------------------------

log "Creating new data directory at $NEW_DATADIR if needed..."
mkdir -p "$NEW_DATADIR"

# Backup existing NEW_DATADIR if it is non-empty
if [ "$(find "$NEW_DATADIR" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)" -gt 0 ]; then
    NEW_BACKUP="${NEW_DATADIR}.preexist-backup-${BACKUP_SUFFIX}"
    log "$NEW_DATADIR is not empty. Moving its contents to $NEW_BACKUP"
    mkdir -p "$NEW_BACKUP"
    mv "$NEW_DATADIR"/* "$NEW_BACKUP"/ 2>/dev/null || true
fi

# --- Backup old data dir --------------------------------------------------

OLD_BACKUP="${OLD_DATADIR}.backup-${BACKUP_SUFFIX}"
log "Backing up old data directory $OLD_DATADIR to $OLD_BACKUP ..."
cp -a "$OLD_DATADIR" "$OLD_BACKUP"

# --- Move data to new location (rsync for safety) ------------------------

log "Syncing data from $OLD_DATADIR to $NEW_DATADIR ..."
if ! command -v rsync >/dev/null 2>&1; then
    err "rsync not found. Install rsync and run again."
    # Restore from backup (best effort)
    log "Restoring from backup..."
    rm -rf "$NEW_DATADIR"/*
    cp -a "$OLD_BACKUP"/* "$OLD_DATADIR"/ 2>/dev/null || true
    exit 1
fi

rsync -aHAX --delete "$OLD_DATADIR"/ "$NEW_DATADIR"/

# --- Fix ownership & perms ------------------------------------------------

log "Setting ownership and permissions on $NEW_DATADIR ..."
chown -R mysql:mysql "$NEW_DATADIR"
chmod 755 /home
find "$NEW_DATADIR" -type d -exec chmod 750 {} \; 2>/dev/null || true
find "$NEW_DATADIR" -type f -exec chmod 640 {} \; 2>/dev/null || true

# --- Replace OLD_DATADIR with symlink ------------------------------------

log "Replacing $OLD_DATADIR with symlink to $NEW_DATADIR ..."

# Move original out of the way (we already backed it up above)
OLD_ORIG="${OLD_DATADIR}.orig-${BACKUP_SUFFIX}"
mv "$OLD_DATADIR" "$OLD_ORIG"

# Create symlink
ln -s "$NEW_DATADIR" "$OLD_DATADIR"

# --- systemd override: ProtectHome & ReadWritePaths ----------------------

OVERRIDE_DIR="/etc/systemd/system/mariadb.service.d"
OVERRIDE_CONF="$OVERRIDE_DIR/override.conf"

log "Configuring systemd override at $OVERRIDE_CONF ..."
mkdir -p "$OVERRIDE_DIR"

cat > "$OVERRIDE_CONF" <<EOF
[Service]
ProtectHome=read-only
ReadWritePaths=$NEW_DATADIR
EOF

log "Reloading systemd daemon..."
systemctl daemon-reload

# --- AppArmor tweak (if profile exists) ----------------------------------

if command -v aa-status >/dev/null 2>&1; then
    if aa-status 2>/dev/null | grep -q "usr.sbin.mysqld"; then
        log "AppArmor profile for mysqld detected. Updating paths..."
        APPARMOR_PROFILE="/etc/apparmor.d/usr.sbin.mysqld"
        if [ -f "$APPARMOR_PROFILE" ]; then
            # Only append if not already present
            if ! grep -q "$NEW_DATADIR/" "$APPARMOR_PROFILE" 2>/dev/null; then
                cat >> "$APPARMOR_PROFILE" <<EOF

# Added by move-mariadb-to-home.sh
$NEW_DATADIR/ r,
$NEW_DATADIR/** rwk,
EOF
                log "Reloading AppArmor..."
                systemctl reload apparmor || true
            else
                log "AppArmor profile already contains $NEW_DATADIR rules."
            fi
        else
            log "AppArmor profile file $APPARMOR_PROFILE not found; skipping."
        fi
    else
        log "No enforcing AppArmor profile for mysqld reported; skipping AppArmor changes."
    fi
else
    log "AppArmor tools not installed; skipping AppArmor changes."
fi

# --- Start MariaDB and verify --------------------------------------------

log "Starting MariaDB with new data location..."
if ! systemctl start mariadb; then
    err "MariaDB failed to start. Attempting rollback..."

    # Stop again just in case
    systemctl stop mariadb || true

    # Remove symlink and restore original dir
    rm -f "$OLD_DATADIR"
    mv "$OLD_ORIG" "$OLD_DATADIR"

    # Restore original override (best effort: just move file away)
    if [ -f "$OVERRIDE_CONF" ]; then
        mv "$OVERRIDE_CONF" "${OVERRIDE_CONF}.failed-${BACKUP_SUFFIX}" || true
        systemctl daemon-reload || true
    fi

    # Try starting MariaDB from original location
    systemctl start mariadb || true

    err "Rollback attempted. MariaDB may be running from the original location."
    err "Check 'systemctl status mariadb' and logs with 'journalctl -u mariadb.service'."
    err "Backup of original data: $OLD_BACKUP"
    exit 1
fi

# --- Final checks ---------------------------------------------------------

log "MariaDB started successfully."

# Test that mysql user can write to new dir
if sudo -u mysql touch "$NEW_DATADIR/.write_test" 2>/dev/null; then
    rm -f "$NEW_DATADIR/.write_test"
    log "Verified mysql user can write to $NEW_DATADIR."
else
    err "Warning: mysql user could not write test file in $NEW_DATADIR."
fi

log "Old original datadir preserved at: $OLD_ORIG"
log "Backup copy of original data at:  $OLD_BACKUP"
log "New data directory in use via symlink: $OLD_DATADIR -> $NEW_DATADIR"

echo "[+] Migration complete."
exit 0

Conclusion

With this script and guide, you now have a repeatable, fault-tolerant way to move MariaDB’s data directory from /var/lib/mysql to /home/mysql on Debian:

Safer than manual copy/paste operations
Automatically handles systemd hardening and AppArmor
Easy to run again on future servers

Feel free to share or adapt this script in your own infrastructure tooling or DevOps playbooks.

Categorized in:

Miscellaneous,

Last Update: December 4, 2025

Tagged in:

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Jaspreet Singh

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