BackupBuddy Exporting Only Main Site Files in Multisite Installations and the Subsite Inclusion Workflow That Solved Missing Data

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WordPress Multisite installations offer a powerful way to manage multiple sites under one umbrella, but with this convenience comes complexity—especially when it comes to backups and migrations. For developers and site administrators using BackupBuddy for this task, a recurring pain point has been the tool’s limitation in exporting only the main site’s files during a Multisite backup. This oversight often leads to frustrating moments when key data from subsites is missing post-migration. However, a workaround and improved workflow for including subsite data has emerged, dramatically improving success rates for full-site restores and migrations.

TL;DR

If you’re backing up a WordPress Multisite using BackupBuddy, you might be capturing only the main site’s files and missing critical data from subsites due to how BackupBuddy structures its exports. This can cause broken links, missing media files, and incomplete functionality when restoring or migrating. Fortunately, by adjusting the backup workflow to include subsite directories manually and using advanced export settings, users can now achieve accurate and complete backups. This article explains why this issue happens and walks through the subsite inclusion workflow that solves it.

What is BackupBuddy?

BackupBuddy, developed by iThemes, is a popular backup and migration plugin used by WordPress site administrators to secure data, create backups, and move sites between servers. With over a million installations, it’s a well-established tool in the WordPress ecosystem.

While BackupBuddy performs excellently in single-site WordPress environments, users often hit roadblocks when extending its functionality to Multisite networks. Specifically, backup files tend to include data and files from only the main site (site ID 1), leaving subsites with missing content, configurations, and media.

The Problem: Missing Subsite Data in Multisite Exports

WordPress Multisite networks are structured around a shared codebase and a central wp-content directory, with subsites differentiated through database tables and media folders. Each subsite typically has:

  • Unique media stored in wp-content/uploads/sites/{site_id}/
  • Separate database tables like wp_{site_id}_posts, wp_{site_id}_options, etc.
  • Custom themes or plugins assigned specifically to that subsite

When using BackupBuddy in a default configuration, it will largely focus on backing up:

  • The main site’s uploads (often in /uploads/)
  • The database without clearly identifying linked subsite tables
  • Core WordPress files and plugins

As a result, when the backup is restored—particularly when migrating to a new host or local server—administrators often find subsites with:

  • Missing images and attachments
  • Corrupted links or “404 Not Found” errors for subsite pages
  • Empty dashboards with no posts or incorrect themes

Why Does This Happen?

Fundamentally, BackupBuddy treats a Multisite installation more like a monolithic entity. Its logic doesn’t fully extend to identifying and exporting the unique identifiers and file paths associated with each subsite. Some of the key reasons include:

  1. Default path exclusions: The wp-content/uploads/sites/ directory where subsite media lives may be excluded if not manually added to the backup.
  2. Database table misalignment: Tables associated with subsites, such as wp_2_posts, are not always flagged automatically for backup inclusion.
  3. Lack of automation: There’s no built-in, automated method in BackupBuddy to iterate through each subsite and pull its specific data independently.

These oversights become larger issues when dealing with a network of tens or hundreds of subsites—an increasingly common architecture for educational institutions, multi-brand corporations, or franchises.

The Subsite Inclusion Workflow That Solved the Problem

To address this, experienced developers have adopted a more comprehensive subsite inclusion workflow that compensates for the limitations in BackupBuddy. This process ensures that each subsite’s core data is accounted for during backup and restoration. The workflow includes the following critical steps:

1. Manually Include Subsite Upload Paths

Navigate to BackupBuddy > Settings > File Settings and manually add the paths to each subsite’s upload folder, typically in this pattern:

wp-content/uploads/sites/2
wp-content/uploads/sites/3
wp-content/uploads/sites/4

This ensures that media for those sites is not left behind when the backup ZIP file is generated.

2. Customize Database Inclusion

Go to Database Settings in BackupBuddy and select custom table inclusion. Manually tick the boxes for subsite-specific tables, which follow this schema:

  • wp_2_posts
  • wp_2_options
  • wp_2_usermeta
  • And so on for each subsite

This step is essential to ensure that BackupBuddy saves the right user data, posts, and settings for each subsite.

3. Verify Themes and Plugins

Some subsites may depend on specific themes or plugins that aren’t active network-wide. BackupBuddy may ignore these if they’re not in use by the main site. Make sure all related themes and plugins are actively included in the backup job.

4. Test Backups in a Staging Environment

Once a backup file is created, restore it in a staging environment to verify that all subsites are functional. Check for:

  • Presence of media in all subsites
  • Page layouts, internal links, and permalink structure
  • User access and content visibility

Alternative Tools and Plugins

While BackupBuddy can be configured to support multisite backups with the right workflow, there are a few other tools that offer better out-of-the-box support for WordPress Multisite:

  • WP Migrate Pro with Multisite Tools Add-On – Offers granular control over migrating specific subsites.
  • All-in-One WP Migration – Works decently with Multisite with extensions, although more limited in features.
  • ManageWP – Cloud-based backup with partial support for Multisite configurations.

However, BackupBuddy remains a strong solution if properly configured, thanks to its scheduling options, local + remote storage support, and full file/database backups.

Summary: Lessons Learned

The limitations of BackupBuddy when exporting multisite data highlight a broader truth: tools are only as effective as the understanding and care we apply when using them. For administrators managing Multisite setups, the keys to full and reliable backups include manual inclusion of subsite directories and tables, active theme/plugin verification, and rigorous testing.

By adapting the backup workflow and adopting a thorough, systematic process, site admins can rest easier knowing their entire network—including every subsite—is properly backed up and ready for recovery.

Final Tips for Multisite Backup Mastery

  • Document everything: Keep a spreadsheet with each site’s ID, custom paths, and plugin dependencies.
  • Automate when possible: Use cron jobs synced to your backup tool for regular file sweeps.
  • Use version control: For themes across subsites, version control like Git can save hours during restoration.

With the right strategy in place, even the complexities of Multisite backups can become manageable—and even predictable.