Full cPanel Backup and Restore Guide: Files, Databases and Emails

Why cPanel Backups Matter More Than You Think

When you manage websites, email and databases on a cPanel hosting account, your data lives on a single server. A failed plugin update, a hacked script, a deleted folder or a corrupted database table can instantly break everything your visitors see. The only thing that truly separates a minor inconvenience from a long, stressful outage is a clean, recent backup that you can restore with confidence.

At dchost.com, we regularly help customers recover entire accounts, individual sites and email inboxes from cPanel backups. The pattern is always the same: those who already have a clear backup routine breathe easily; those who do not, lose time and sleep. This guide is written to put you firmly in the first group.

We will walk through what a full cPanel backup actually includes, how to back up files, databases and emails step by step, where to store backups, and how to restore them safely. Whether you run a single business site, multiple client projects or an email-heavy domain, this article will give you a practical, repeatable backup and restore workflow you can trust.

What a Full cPanel Backup Actually Contains

Before you click any buttons, it helps to understand what a cPanel backup is and what it is not. A full cPanel backup taken from within your account is essentially a compressed archive of everything tied to that cPanel user.

A typical full backup contains:

• Home directory files: All website files (public_html and subdirectories), custom scripts, uploaded media, configuration files, logs (depending on settings) and user-level config.
• Databases: All MySQL/MariaDB databases attached to the account, including content, users and privileges.
• Email data: Mailboxes, email folders (Inbox, Sent, custom folders), email accounts, forwarders and filters.
• DNS zone settings (when cPanel manages DNS): Zone file for your domains, addon domains and subdomains.
• FTP accounts and settings: Additional FTP users and their directory mappings.

In other words, a full cPanel backup is your hosting account in a single file, ready to be restored on the same server or migrated to another cPanel server.

A few important clarifications:

• Backups are not snapshots of the whole physical server. They include only your cPanel account, not other customers or system-level services.
• Full backups cannot usually be restored by end users from inside cPanel. They are meant to be restored by a server administrator (for example via WHM). For partial restores, cPanel gives you self-service tools.
• Backups reflect the exact state of your account at the moment they were created. Anything changed after that point will not be in the backup file.

Knowing this helps you decide when a full backup is appropriate (for example, before a big migration) and when partial backups of files, databases or email will be enough.

Backup Types in cPanel: Full vs Partial

cPanel offers two main backup paths:

• Full Account Backups
• Partial Backups: Home directory, individual databases, email forwarders and filters

Full Account Backup

Full account backups are created from the Backup or Backup Wizard interface in cPanel. They include everything under your account and are ideal when:

• You are migrating your account to another cPanel server (for example, to a new plan at dchost.com).
• You are making major structural changes (rebuilding the site, changing CMS, hosting multiple new applications).
• You want a periodic full archive (e.g. monthly) of the entire environment for long-term retention.

Limitations to keep in mind:

• Full backups are resource-heavy and can take time on large accounts.
• Most shared hosting environments (including ours) do not allow you to restore a full backup file by yourself; restoration is done by support or through WHM on reseller/VPS/dedicated setups.

Home Directory Backup

A Home Directory backup is a partial backup that includes:

• All website files (public_html, subdomains, addon domains)
• Custom folders in your home directory that belong to your web apps

It does not include databases or email messages; those are backed up separately. Use a home directory backup when:

• You are making file-level changes (theme updates, plugin uploads, code deployments).
• You want a quick snapshot of your site’s files without touching email or databases.

Database Backups

cPanel lets you download individual database backups (as .sql.gz files) or export via phpMyAdmin. You should back up databases before:

• Applying major CMS or plugin updates (WordPress, Joomla, Drupal, etc.).
• Running SQL scripts that change schema or bulk data.
• Cleaning up or optimizing large tables.

For WordPress users, combining database backups with file backups is essential. Our article on WordPress backup strategies on shared hosting and VPS dives deeper into CMS-specific scenarios.

Email Forwarders and Filters

In the backup interface you will also see options to back up and restore Email Forwarders and Email Filters. These are configuration settings, not the email content itself. Use them when:

• You rely on complex forwarding rules (support queues, distribution lists).
• You have custom filters and want to preserve them during migrations.

The actual email messages (Inbox, Sent, folders) are part of the full backup and home directory backup. You can also extract them manually if needed, as we will see later.

Preparing Your Account for Safe Backups

Good backups start with a bit of housekeeping. Taking a backup of a messy account is better than no backup at all, but a few simple steps will make your backups quicker, smaller and easier to restore.

Check Disk Usage and Quotas

Backups need disk space to be created and stored. In cPanel:

1. Log in to cPanel.
2. Look at the Disk Usage or Statistics panel to see how much space you are using vs. your quota.
3. If you are close to your limit, clean up unnecessary files (old backups, staging sites, logs).

If you regularly hit disk limits, you may need a plan with more storage or a VPS/dedicated server. Our team at dchost.com can help you choose a package that fits your backup and growth needs.

Remove Old Local Backups and Temporary Files

Many site owners unintentionally keep multiple .zip or .tar.gz backup files inside their home directory. When you run a new full backup, these files are included again, wasting space and time.

Before creating a fresh backup:

• Delete old backup archives you no longer need from your account (after ensuring they are safely stored elsewhere).
• Remove unused staging folders and very old test sites.
• Empty cache directories created by plugins (if safe to do so) to reduce size.

Enable SSL and Review DNS Before Major Changes

If you are about to perform a migration or big change, verify that your DNS and SSL configuration is healthy first. Two useful resources from our blog:

• If you are unsure about DNS records, see what DNS records are and how A, AAAA, CNAME, MX, TXT and SRV work.
• To understand free SSL certificates and how to set them up on cPanel, read our Let’s Encrypt SSL setup guide for cPanel.

Backing up a clearly configured environment makes restores much less confusing later.

Step-by-Step: Creating a Full cPanel Backup

Let’s walk through the process of creating a full account backup from the standard cPanel interface. Exact menu names may vary slightly depending on the theme, but the flow is the same.

1. Log In and Open the Backup Tool

1. Log in to your cPanel account.
2. In the Files section, click either Backup or Backup Wizard. We will focus on the regular Backup interface first.

2. Generate a Full Backup

1. In the Backup interface, look for the section labeled Full Backup.
2. Click Download a Full Account Backup or Generate a Full Backup (depending on your cPanel theme).

3. Choose Backup Destination

cPanel will ask where you want to store the backup:

• Home Directory: The backup file is generated inside your existing account (usually in /home/username). You will then download it via browser or FTP.
• Remote FTP Server: The backup is sent over FTP to a remote server you specify.
• Remote FTP Server (Passive Mode Transfer): Same as FTP, but in passive mode, useful if firewalls block active FTP.
• Secure Copy (SCP): Sends the backup via SSH to a remote destination using SCP.

For most users, selecting Home Directory and then downloading the backup is the simplest approach. For more advanced setups, sending backups directly to a remote storage server is ideal and aligns well with a 3-2-1 strategy. We discuss that more in our article on the 3-2-1 backup strategy and automated backups on cPanel, Plesk and VPS.

4. Enter Email Notification (Recommended)

You will see a field labeled Email Address for completion notification:

• Enter an email address you monitor actively.
• Or select Do not send email notification of backup completion if you prefer to check manually.

On large accounts, backups can take quite a while. The email confirmation helps you avoid downloading an incomplete file.

5. Start the Backup and Wait

1. Click Generate Backup.
2. cPanel will start assembling all files, databases and email data into a compressed archive.
3. Once finished, you will either receive an email, or you can refresh the page to see the backup file listed for download.

The file name will usually look like: backup-YYYY-MM-DD_HH-MM-SS_username.tar.gz.

6. Download and Store Offsite

After the backup is ready:

• Click the file name to download through your browser; or
• Use SFTP/FTP to download the file from your home directory to your local machine.

Do not leave full backups sitting in your account indefinitely. After you download and verify them, move them to offsite storage (your workstation, an encrypted external drive, or object storage) and optionally delete them from the server to free space.

Backing Up Files, Databases and Emails Individually

Full backups are great for big milestones and migrations, but in daily operations you often only need partial backups. cPanel makes it easy to grab just the bits you care about.

Home Directory (Website Files) Backup

1. In cPanel, go to Files > Backup.
2. Under Partial Backups, find Home Directory.
3. Click Download. cPanel will generate and serve a compressed archive of your home directory.

Use this:

• Before deploying new code or themes.
• Before using the File Manager to perform bulk deletions or moves.
• Before enabling aggressive caching plugins that may change file structures.

Database Backups via cPanel

1. In cPanel, go to Files > Backup or Files > Backup Wizard.
2. Under Partial Backups, look for Download a MySQL Database Backup.
3. Click the name of the database you want to back up (e.g., user_wp123).
4. Your browser will download a .sql.gz file.

Alternative via phpMyAdmin:

1. In cPanel, open Databases > phpMyAdmin.
2. Select your database on the left.
3. Click the Export tab.
4. Choose Quick and SQL, then click Go.

For WordPress or database-intensive applications, we strongly recommend combining these backups with a regular schedule, as covered in our backup and data retention best practices for SaaS apps. The principles apply equally well to content-heavy websites.

Email Data Backups

There are three layers to email backups with cPanel:

• Account configuration: email accounts, passwords, forwarders, filters
• Server-side mailboxes: the actual message files stored in your home directory
• Client-side copies: if you use POP3/IMAP in a desktop client

1. Forwarders and Filters

1. Go to Files > Backup.
2. Under Partial Backups, find Email Forwarders & Filters.
3. Download the Forwarders and Filters backups.

2. Server-Side Mailboxes

Mailboxes live in your home directory under mail/ and etc/. They are automatically included in:

• Full cPanel backups
• Home directory backups

You rarely need to back them up separately, unless you are doing something very custom. However, understanding how you access email matters a lot for backup strategy. If you are unsure about POP3 vs IMAP vs webmail, our article comparing POP3, IMAP and webmail for backup and access is worth a read.

3. Client-Side Copies (Outlook, Thunderbird, Apple Mail)

If you use POP3 with “delete from server” enabled, your desktop or laptop may be the only place where some emails exist. In that case you must:

• Regularly back up your mail client profiles (PST/OST files for Outlook, Thunderbird profiles, etc.).
• Consider switching to IMAP, which keeps the master copy on the server and simplifies server-side backups.

Automating Backups with Cron Jobs and Offsite Storage

Manual backups are good, but one missed click can coincide with the one incident you actually care about. Automation turns backup from a task you remember “when there’s time” into a reliable, invisible safety net.

cPanel’s Built-In Automatic Backups

On many shared hosting plans, backups are automatically scheduled at the server level by the provider. At dchost.com, we design our backup schedules to balance safety and performance; however, you should always ask support exactly what is backed up, how often and how long it is kept.

Key questions to clarify with your provider (or your own DevOps team if you run a VPS/dedicated server):

• Frequency: daily, weekly, monthly?
• Retention: how many days of history?
• Scope: full accounts, only files, only databases?
• Location: stored on the same server or offsite?

Even if automatic provider backups exist, we still recommend having your own independent backups, especially for critical business or customer data.

Cron Jobs and Custom Backup Scripts (VPS / Dedicated)

If you manage a VPS or dedicated server with root access, you can configure cron jobs to:

• Run cPanel/WHM backup routines at specific times.
• Export individual databases on a schedule.
• Sync backup archives to remote storage via rsync, rclone or S3-compatible tools.

We have a detailed walkthrough on this in our article planning automatic tasks with cron jobs on cPanel and DirectAdmin. It shows how to schedule backups, reports and maintenance tasks cleanly.

Offsite and Versioned Backups

Regardless of your hosting type (shared, VPS, dedicated or colocation), your backup plan is strongest when it follows the 3-2-1 principle:

• 3 copies of your data
• 2 different media (e.g., server disk + external disk/object storage)
• 1 copy offsite (physically separate from your main server or data center)

For example, you might keep:

• The live data on your cPanel account.
• Daily backups on a separate backup server maintained by dchost.com.
• Weekly or monthly archives in S3-compatible storage or another region.

If you are not yet doing offsite backups and want a practical, step-by-step starting point, our guide on offsite backups with Restic/Borg to S3-compatible storage pairs nicely with the cPanel-level routines described here.

Restoring from cPanel Backups Safely

Backups are only as good as your ability to restore them calmly when needed. cPanel offers self-service restore options for partial backups; full backup restores generally require administrator access.

Important General Rules Before Any Restore

• Always create a fresh backup of the current state before restoring an older one. That way, you can roll back if needed.
• Plan for downtime for the specific sites or services you are restoring, especially databases and email.
• Communicate with your team or clients so they know not to make changes during the restore window.

Restoring a Full cPanel Backup

End users usually cannot restore a full backup from within cPanel. Instead, there are two typical scenarios:

• Same server restore: Your hosting provider (or you, if you have WHM/root access) uses the full backup file to restore your entire account to an earlier state.
• Migration to another server: The full backup is uploaded to a new cPanel server and restored there to move your site and email with minimal changes.

If you are on shared hosting at dchost.com, open a support ticket and provide the path or upload location of your full backup. Our team will schedule the restore and confirm the scope (all data, or limited parts) and timing with you.

Restoring Home Directory (Files)

1. Log in to cPanel.
2. Go to Files > Backup.
3. Under Restore a Home Directory Backup, click Choose File.
4. Select the previously downloaded home directory backup (.tar.gz file).
5. Click Upload.

cPanel will extract the archive and overwrite existing files with the copies from the backup. Newer files that do not exist in the backup may be left untouched, but you should assume that anything with the same name will be replaced.

Tips:

• If you only need to restore a single folder or file, consider extracting the backup locally and uploading just that part via FTP or File Manager instead of restoring the whole home directory.
• For CMS sites (WordPress, etc.), be careful not to mix files from different plugin/theme versions; ideally restore both files and the matching database backup from the same time.

Restoring Databases

You can restore databases either via the Backup interface or via phpMyAdmin.

Method 1: Using the Backup Interface

1. In cPanel, go to Files > Backup.
2. Under Restore a MySQL Database Backup, click Choose File.
3. Select the .sql.gz file you previously downloaded.
4. Click Upload.

This will restore the database with the same name, overwriting its contents with the backup. Make sure you know which application uses which database; mixing them up can break sites.

Method 2: Using phpMyAdmin

1. In cPanel, open Databases > phpMyAdmin.
2. Select the target database on the left.
3. Click the Import tab.
4. Click Choose File and select your .sql or .sql.gz backup file.
5. Leave defaults unless you know you need specific settings.
6. Click Go to start the import.

phpMyAdmin will recreate tables and data from the backup file. If the database already contains data, it will generally be replaced or merged depending on the backup contents. To avoid conflicts, many administrators first drop the existing tables (or create a new empty database) before import, but this must be done carefully.

Restoring Email Forwarders and Filters

1. In cPanel, go to Files > Backup.
2. Under Restore Email Forwarders or Restore Email Filters, click Choose File.
3. Select the backup file you downloaded earlier.
4. Click Upload.

The existing forwarders or filters may be merged with the restored ones, but depending on your cPanel version, some settings might be overwritten. After the restore, verify your critical routing rules in the Email > Forwarders and Email > Email Filters sections.

Restoring Email Messages

If you lost email content (not just configuration), the options depend on your situation:

• Home directory backup or full cPanel backup available: Ask your provider (or use SSH if you have root) to restore only the mail directories (usually under /home/username/mail/domain/user/). On shared hosting, this is typically a provider task.
• IMAP client still has messages: You may be able to resync from your mail client to the server by copying folders back to the IMAP account after it is recreated.
• POP3-only setup: Your best hope is restoring from local mail client backups (PST/OST, etc.).

Because email can be tricky to reconstruct, we strongly recommend treating email backups as seriously as website backups, especially for sales and support inboxes.

Testing, Verifying and Maintaining Your Backup Plan

The last step — and the one most often skipped — is verifying that your backup plan actually works when you need it. At dchost.com, we treat restores as part of the backup process itself.

Run Periodic Restore Tests

At least a few times per year, or after any major change in your site architecture, perform a controlled restore test:

• Create a staging subdomain (e.g., staging.example.com) or use a separate cPanel account.
• Restore a recent home directory and database backup there.
• Update the staging site’s configuration (database credentials, URLs) as needed.
• Navigate the site and check that key flows (login, checkout, forms) work.

This not only validates the backups themselves but also gives you a clear, rehearsed procedure for real incidents. For a broader view on disaster recovery planning, our article on writing a no-drama DR plan with RTO/RPO and backup tests is a good companion read.

Keep a Simple Backup Runbook

Document your backup routine in a small internal guide, for example:

• When full cPanel backups are created (monthly/quarterly)
• When partial backups (files, databases) are created (e.g., daily for DB)
• Where each type of backup is stored (folder paths, remote endpoints)
• Who is responsible for checking backup completion emails
• How to request a full restore from your provider

When team members change or your infrastructure grows (more cPanel accounts, VPS, dedicated servers), this small runbook saves a lot of confusion.

Common Mistakes to Avoid

• Relying solely on provider backups without having your own copies or knowing the retention policy.
• Storing all backups on the same server as the live sites; a hardware issue or ransomware event can take everything at once.
• Not including databases in your backup schedule for CMS-driven sites.
• Keeping only one backup copy that silently becomes corrupted or incomplete.
• Never testing restores until the day something breaks in production.

Wrapping Up: Build a Backup Habit, Not a One-Time Task

cPanel gives you everything you need to protect your files, databases and emails — but the responsibility to use those tools consistently is still on you. A full cPanel backup is your safety net for big changes and migrations; partial backups of the home directory, individual databases and email settings are your daily armor against smaller incidents and human mistakes.

If you combine those tools with a realistic schedule, offsite storage and occasional restore tests, you move from hoping things will be fine to knowing you can recover. That peace of mind is exactly why, at dchost.com, we emphasize backup planning in every hosting, VPS, dedicated and colocation conversation we have with customers.

If you are unsure whether your current hosting plan, disk space or backup setup is enough for your growth, reach out to our team. We can help you design a practical cPanel backup routine, choose the right infrastructure and make sure that when something does go wrong, your data — and your business — stay safe.