Fix Wrong Disk Quotas on a cPanel Server (Root)

cPanel relies on file system quotas to show disk usage and enforce package limits. If quotas are off or out of sync, accounts show 0 MB used, unlimited space, or wrong numbers, and resellers can no longer trust their usage reports.

MdmHost maintains quotas on its hosting plans. This guide is for administrators of their own cPanel server with root access.

Before you start

Root access to WHM and SSH.
Know your file system: df -T /home shows whether /home is XFS or ext4.
A maintenance window if a reboot may be needed (XFS).

Symptoms

List Accounts shows 0 or unlimited disk used for accounts with data.
Accounts exceed their quota without being stopped.
Users see different numbers in cPanel's Statistics and Disk Usage tool.

Enable quotas initially

On a new server, run WHM → Server Configuration → Initial Quota Setup, or from SSH:

/usr/local/cpanel/scripts/initquotas

On XFS, quotas must be enabled as a mount option (uquota or usrquota) and for the root file system in the kernel boot parameters (rootflags=uquota); the script tells you if a reboot is required.

Warning: Editing /etc/fstab or boot parameters incorrectly can stop the server from booting. Keep console access available and back up the files first.

Repair quotas

/usr/local/cpanel/scripts/fixquotas

The script recalculates usage for every account and reapplies package limits. It can take a long time on large servers; run it in screen.

Check one account

quota -s -u username
repquota -s /home | head

Compare the result with what WHM shows in List Accounts.

Common causes of wrong numbers

Files owned by the wrong user, for example after a manual restore, count against another account or none. Fix ownership with chown -R username:username /home/username for files that belong to the user (careful with public_html group ownership, which is often nobody).
Mail and databases: database files in /var/lib/mysql are counted only if cPanel's database usage tracking is enabled in Tweak Settings (see Tweak Settings).
Usage is cached and refreshed periodically, so very recent changes may not show yet.

After fixing

Check accounts over quota in WHM → Account Information → Show Accounts Over Quota.
Tell affected customers before their sites start hitting limits again (see monitoring usage).

Frequently asked questions

Does fixquotas cause downtime?

No, sites keep running. It uses disk I/O, so run it at a quiet time.

Why do inodes matter too?

Quotas can also limit the number of files. Many small files, such as cache folders, can hit inode limits before disk limits (see the inode guide for users).

Are CloudLinux limits related?

No. CloudLinux limits CPU, memory and I/O speed; disk space comes from file system quotas.

How often should I run fixquotas?

Only when numbers look wrong, after restores or file system changes. cPanel keeps quotas updated automatically otherwise.

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