A Guide to the cPanel & WHM Backup Folder Structure

When you configure automated backups in WebHost Manager (WHM), cPanel creates a highly organized directory structure at your chosen destination. Understanding this structure is crucial for manually locating backups, verifying their integrity, and performing restores. This guide breaks down the folder hierarchy you will find, whether your backups are stored locally on the server or on a remote SFTP location.

The Top-Level Structure: Retention and Dates

The foundation of the WHM backup system is built around your retention policy (daily, weekly, monthly). The backup destination’s root folder will contain a series of directories named after the date the backup was created or the retention period it represents.

A typical backup destination might look like this:

/backup_destination/
├── 2025-09-17/
├── 2025-09-16/
├── 2025-09-15/
├── weekly/
├── monthly/
└── .meta/

/backup_destination/: This is the main folder you specified in WHM » Backup Configuration. A common local path is /backup.
YYYY-MM-DD/: These folders contain the daily backups. WHM keeps a specific number of these based on your settings before deleting the oldest ones.
weekly/ and monthly/: These folders store the backups that have been promoted to weekly or monthly retention status. They contain the same internal structure as the daily folders.
.meta/: This hidden folder contains metadata that helps WHM track the status and history of backup runs.

Anatomy of a Daily Backup Folder

The real organization happens inside each date-stamped folder (e.g., 2025-09-17/). This is where the data for every account, along with system files, is stored for that specific day.

Here is a visual representation of the structure inside a daily backup folder:

/backup_destination/2025-09-17/
│
├── accounts/
│ ├── userone/
│ │ └── userone.tar.gz
│ ├── usertwo/
│ │ └── usertwo.tar.gz
│ └── … (a folder for every cPanel account)
│
├── system/
│ ├── nobody.sql
│ ├── pkgacct.versions
│ └── … (system-wide configurations and databases)
│
├── dirs/
│ └── … (metadata used for incremental backups)
│
└── cpbackup-exclude.conf

A Guide to the cPanel & WHM Backup Folder Structure