1. First check whether quota is enabled for /home partition.
# vi /etc/fstab
LABEL=/home /home ext3 defaults,usrquota 1 2
2. Then remount the /home partition
# mount -o remount /home
3. The we need to create a file called aquota.user for that we need to run quotacheck
# quotacheck -c /home
4. Then we need to enable quota
# quotaon /home
4 a). Thats it this will enable quota on /home. Now you can edit the quota of a user using this
# edquota <username>
5) Run /scripts/fixquotas this will solve the quota issue of cpanel accounts.
6) After this `repquota -a` should print out the soft/hard limits with grace periods for all users. If quotas are still not reporting anything in WHM and/or CPanel, check
# repquota -a
7) /var/cpanel/cpanel.config for disablequotacache=0
If that is set to 0, try setting it to 1 and see if that fixes it.
# vi /var/cpanel/cpanel.config ; /scripts/fixquotas
8) If a user’s quota shows more space being used than is in their home directory chances are there
are stray files on the system owned by their UID. To find these files, run the following as root:
# find / -user username -ls
Depending on what that turns up, you should either chown those files to the
correct user or delete them.