How to Clean Up Unused Docker Volumes and Images on Your Coolify VPS

If your VPS is running low on disk space, Docker and Coolify might be the culprits. Over time, old containers, volumes, and images pile up and eat away at your storage. This guide will walk you through finding and removing these space hogs safely and easily.

What You'll Learn

• How to find what's taking up space on your server

• How to identify and remove unused Docker volumes

• How to use an automated script to clean up Docker overlay files

• How to perform a complete system cleanup

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Part 1: Find What's Using Your Disk Space

Step 1: Install NCDU (Disk Usage Analyzer)

First, we need a tool that shows us exactly where our storage is going.

sudo apt install ncdu

What this does: Installs NCDU, a simple program that scans your disk and shows which folders are using the most space.

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Step 2: Scan Your Entire System

Now let's scan the whole server to see where space is being used.

sudo ncdu /

What this does: Starts scanning from the root directory (/) and builds a visual map of your disk usage. This might take a few minutes depending on how much data you have.

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Step 3: Navigate and Explore

Once the scan finishes, you'll see a list of directories with their sizes.

How to use it:

• Use arrow keys to move up and down

• Press Enter to dive into a folder

• Press d to delete a file (be careful!)

• Press q to quit

Where to look: The biggest storage directories are usually:

• /var/lib/docker/volumes - Old database and app data

• /var/lib/docker/overlay2 - Leftover container files

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Step 4: Identify Problem Files

Navigate into these Docker directories and look for:

• Volumes from deleted apps

• Old database folders (like ClickHouse, PostgreSQL, etc.)

• Containers you're no longer using

Example: In my case, I found old ClickHouse volumes taking up 15GB that should have been deleted when I removed the app.

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Step 5: Remove Specific Volumes Manually

If you found a volume you want to delete, use this command:

docker volume rm volume_name_here

Example:

docker volume rm v8swk8w04k048wc80w8kw8gk_langfuse-clickhouse-logs

What this does: Permanently deletes the specified Docker volume. Make sure you don't need the data before running this!

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Part 2: Use the Automated Docker Cleanup Script

Manual cleanup is good, but there's a faster way to clean up Docker's hidden overlay files.

Step 1: Download the Cleanup Script

curl -L -o docker-pruner.sh https://gist.githubusercontent.com/fayak/3a438426a906d9b85b68bc38ead6d5bb/raw

What this does: Downloads a specialized script that finds and removes unused Docker overlay directories (leftover files from old containers).

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Step 2: Make the Script Runnable

chmod +x docker-pruner.sh

What this does: Gives the script permission to run on your system.

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Step 3: See What Will Be Deleted (Safe Preview)

Before deleting anything, let's see what the script found:

sudo ./docker-pruner.sh list

What this does: Shows you all the unused overlay directories that are safe to delete. No changes are made yet—this is just a preview.

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Step 4: Test Safely with Markers (Recommended)

This optional step adds an extra safety check:

sudo ./docker-pruner.sh marker

What this does: Places a temporary marker file in each unused directory to track them.

Then check if any running containers are using those directories:

sudo ./docker-pruner.sh check

What this does: Verifies that no active containers or images depend on those directories. If you see "Problem detected!", don't proceed—restart the affected containers first.

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Step 5: Run the Cleanup

If everything looks good, it's time to clean up:

sudo ./docker-pruner.sh clear

What this does: Deletes all the unused overlay directories, freeing up disk space immediately.

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Step 6: Complete System Cleanup

Finish with Docker's built-in cleanup commands:

sudo docker system prune -af --volumes

What this does: Removes:

• All stopped containers

• All unused networks

• All dangling images

• All unused volumes

Then clear the build cache (if you build Docker images):

sudo docker builder prune -f

What this does: Removes old build cache files that Docker keeps when building images.

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Final Tips

✅ Check your disk space before and after with df -h to see how much you freed up

✅ Run cleanup regularly - Set a monthly reminder to prevent storage issues

✅ Be careful with volumes - Always verify you don't need the data before deleting volumes

✅ Back up important data - Before any major cleanup, back up critical databases and files

⚠️ Never delete volumes from running apps - Always stop or remove apps through Coolify first

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Quick Reference Commands

# Check disk space
df -h

# Scan disk usage
sudo ncdu /

# Remove specific volume
docker volume rm <volume_name>

# List all volumes
docker volume ls

# Complete cleanup (use with caution)
sudo docker system prune -af --volumes