WordPress Multisite Backup Guide: Network and Site-Specific Backups

WordPress Multisite transforms a single WordPress installation into a network of multiple sites, all sharing the same WordPress core, plugins, and themes while maintaining separate content and settings. This architecture creates unique backup challenges—how do you backup an entire network versus individual sites? What about shared vs site-specific data? How do you restore one subsite without affecting others?

This comprehensive guide addresses all aspects of WordPress multisite backups using Backup Copilot Pro. You’ll learn the fundamental differences between network-wide and site-specific backups, understand multisite database architecture, and implement backup strategies that protect your entire network while allowing granular control over individual sites.

By the end of this tutorial, you’ll have a complete multisite backup strategy that protects network admins, subsite owners, and all content across your WordPress network, whether you’re running a small business with 5 sites or an enterprise network with hundreds of subsites.

What You’ll Learn

Understanding WordPress multisite architecture
Network-wide vs site-specific backups
Backing up individual subsites
Restoring multisite networks
Multisite backup best practices
Managing storage for large networks
Converting single site to multisite

Understanding WordPress Multisite

Multisite Architecture Overview

What is WordPress Multisite: WordPress Multisite is a feature that allows you to create and manage multiple WordPress sites from a single WordPress installation. All sites share:

WordPress core files (wp-admin, wp-includes)
Plugins directory (though plugins can be activated per-site)
Themes directory (though themes can be activated per-site)
Database instance (with site-specific table prefixes)

Common Multisite Use Cases:

Corporate networks: Main site + departmental blogs
Educational institutions: University site + faculty/student blogs
SaaS platforms: Service site + customer subsites
Publishing networks: Parent publication + niche topic sites
Franchise businesses: Corporate site + location-specific sites

Multisite Types:

Subdomain Multisite:

Main site: example.com
Subsite 1: blog.example.com
Subsite 2: shop.example.com
Requires wildcard DNS setup

Subdirectory Multisite:

Main site: example.com
Subsite 1: example.com/blog/
Subsite 2: example.com/shop/
Easier to set up, no DNS changes needed

Domain Mapping:

Main site: company.com
Subsite 1: brand1.com (mapped)
Subsite 2: brand2.com (mapped)
Requires domain mapping plugin

Shared vs Site-Specific Data

Understanding what’s shared vs site-specific is critical for backup strategies.

Shared Across All Sites:

WordPress core files (/wp-admin/, /wp-includes/)
All plugins in /wp-content/plugins/
All themes in /wp-content/themes/
Network-level settings and configuration
Network-activated plugins
Super Admin accounts

Site-Specific Data:

Posts, pages, comments (in database)
Uploaded media files (in /wp-content/uploads/sites/[site-id]/)
Site-specific settings and options
Active theme per site
Activated plugins per site
Site administrators and users
Categories, tags, custom taxonomies

Implication for Backups:

Full network backup includes shared + all site-specific data
Individual site backup must include shared components for restoration
Cannot restore single site database without shared tables

Multisite Database Structure

Standard WordPress Tables:

wp_users – All network users (shared)
wp_usermeta – User metadata (shared)

Network-Specific Tables:

wp_blogs – List of all sites in network
wp_site – Network configuration
wp_sitemeta – Network-wide options
wp_registration_log – New site registrations
wp_signups – User/site signup queue

Main Site Tables (Site ID 1):

wp_posts, wp_postmeta
wp_comments, wp_commentmeta
wp_terms, wp_term_taxonomy, wp_term_relationships
wp_options
And all other standard WordPress tables

Subsite Tables (Site ID 2, 3, etc.): Each subsite gets its own set of tables with numbered prefix:

wp_2_posts, wp_2_postmeta
wp_2_comments, wp_2_commentmeta
wp_2_options
And so on for each site

Example 3-Site Network:

Network tables: wp_blogs, wp_site, wp_sitemeta
Shared tables: wp_users, wp_usermeta
Main site (ID 1): wp_posts, wp_options, etc.
Subsite (ID 2): wp_2_posts, wp_2_options, etc.
Subsite (ID 3): wp_3_posts, wp_3_options, etc.
Total: ~60+ tables for 3 sites

Uploads Directory Structure

Multisite Uploads Organization:

/wp-content/uploads/
├── sites/
│   ├── 2/
│   │   ├── 2025/
│   │   │   ├── 01/
│   │   │   │   ├── image1.jpg
│   │   │   │   └── document.pdf
│   │   │   └── 02/
│   │   └── file-manager/
│   ├── 3/
│   │   ├── 2025/
│   │   │   └── 01/
│   │   │       └── photo.png
│   │   └── woocommerce_uploads/
│   └── 4/
│       └── 2024/
├── 2025/        (main site uploads)
│   └── 01/
└── 2024/        (main site uploads)

Key Points:

Main site (ID 1): Files in /uploads/ root
Subsites: Files in /uploads/sites/[site-id]/
Each site can have plugins with custom upload folders
Total uploads size = sum of all sites + main site

Backup Strategies for Multisite

Network-Wide Backups

What’s Included:

Complete database (all network, shared, and site tables)
All WordPress core files
All plugins and themes
All uploads from all sites (main + subsites)
wp-config.php and .htaccess

When to Use:

Before WordPress core updates
Before network-wide plugin updates
Before major network configuration changes
For complete disaster recovery
When migrating entire network to new host

Pros:

Complete protection of entire network
One backup for everything
Simplifies restoration process
Ensures network consistency

Cons:

Large file sizes (GB to tens of GB)
Long backup creation time
Longer download/upload times to cloud
Higher storage costs

Recommended Frequency:

Small networks (2-5 sites): Daily
Medium networks (6-20 sites): Weekly
Large networks (21+ sites): Monthly

Site-Specific Backups

What’s Included:

Site-specific database tables only
Site-specific uploads folder only
Optionally: Shared tables needed for restoration
Optionally: Plugins and themes (shared components)

When to Use:

Before updating content on specific site
Before testing plugins on one site
For client accountability (backup their specific site)
To restore individual site without affecting others
To migrate single site out of network

Pros:

Smaller file sizes (MB to few GB)
Faster backup creation
Lower storage costs
Granular control
Can restore one site without touching others

Cons:

Doesn’t include shared components (plugins, themes)
Need network tables for full restoration
More complex restoration process
Potential version mismatches if restoring old subsite backup

Recommended Frequency:

Active sites: Daily
Static sites: Weekly
Development sites: Before major changes

Selective Backup Approach

Recommended Strategy (Best of Both):

Tier 1 – Network-Wide Full Backup:

Frequency: Weekly (Sunday 2 AM)
Includes: Everything (database + all files)
Retention: Last 8 backups (2 months)
Purpose: Disaster recovery, migration

Tier 2 – Daily Network Database Backup:

Frequency: Daily (3 AM)
Includes: Complete database only
Retention: Last 30 backups (1 month)
Purpose: Quick content recovery

Tier 3 – Site-Specific Backups:

Frequency: Before major site changes (manual)
Includes: Site tables + site uploads
Retention: Last 5 per site
Purpose: Individual site rollback

Storage Impact Example (10-site network):

Network full backup (5 GB): 8 backups = 40 GB
Network database (100 MB): 30 backups = 3 GB
Site-specific (200 MB each): 5 per site × 10 sites = 10 GB
Total: ~53 GB cloud storage needed

Creating Multisite Backups

Backing Up the Entire Network

Using Backup Copilot Pro:

Navigate to Backup Copilot in Network Admin
- Important: Must be in Network Admin dashboard, not individual site admin
- URL typically: https://example.com/wp-admin/network/
Click Create Backup tab
Select backup components:
- ✅ Database: All network and site tables
- ✅ wp-content: All plugins, themes, uploads (all sites)
- ✅ wp-config.php: Network configuration
- ✅ .htaccess: Multisite rewrites
Add descriptive note:
- Example: “Full network backup before WP 6.5 update”
Click Create Backup
Monitor progress:
- Large networks may take 10-30 minutes
- Progress bar shows current operation
- Don’t close browser until complete
Verify completion:
- Success message appears
- Backup listed in Manage Backups table
- Check file size is reasonable (several GB for large networks)

What Gets Created:

[uuid].sql – Full database export (~100 MB for 10-site network)
[uuid].zip – wp-content + wp-config + .htaccess (~5+ GB for large networks)

Backing Up Individual Sites

Method 1: Using Backup Copilot Pro (If Supported):

Switch to individual site admin:
- Network Admin > Sites > Click site name > Dashboard
- Or navigate directly to site admin URL
Go to Backup Copilot (site-level, not network)
Enable “Site-Specific Backup Mode” if available
Select components:
- ✅ Site Database Tables: Only tables for this site (wp_X_*)
- ✅ Site Uploads: Only /uploads/sites/X/ folder
- ⚠️ Include Shared Tables: Recommended for restoration
- ⚠️ Include Network Tables: Recommended for restoration
Create backup as normal

Method 2: Manual Site Export:

If plugin doesn’t support site-specific backups:

Database:

Access phpMyAdmin
Select only tables for specific site:
- For site ID 2: wp_2_posts, wp_2_options, etc.
- Plus shared: wp_users, wp_usermeta
- Plus network: wp_blogs, wp_site, wp_sitemeta
Export selected tables

Files:

Use FTP/SFTP
Download /wp-content/uploads/sites/2/ (for site ID 2)
Optionally download plugins and themes

Method 3: WP-CLI (Advanced):

# Export single site database
wp db export site-2-backup.sql --tables=$(wp db tables --all-tables-with-prefix --format=csv --url=site2.example.com)

# Backup site uploads
tar -czf site-2-uploads.tar.gz wp-content/uploads/sites/2/

What Gets Included

Network-Wide Full Backup Includes:

Database (Complete):

Network tables: wp_blogs, wp_site, wp_sitemeta
Shared tables: wp_users, wp_usermeta
Main site tables: wp_posts, wp_options, etc.
All subsite tables: wp_2_posts, wp_3_posts, etc.

Files (Complete):

WordPress core: /wp-admin/, /wp-includes/
All plugins: /wp-content/plugins/
All themes: /wp-content/themes/
Main site uploads: /wp-content/uploads/(year folders)
All subsite uploads: /wp-content/uploads/sites/2/, /sites/3/, etc.
Configuration: wp-config.php, .htaccess

Site-Specific Backup Should Include:

Minimum (Site Restoration Only):

Site-specific tables: wp_X_* where X = site ID
Site-specific uploads: /wp-content/uploads/sites/X/

Recommended (Standalone Restoration):

All of above
Shared tables: wp_users, wp_usermeta (for user accounts)
Network tables: wp_blogs, wp_site (for context)
Active plugins and themes (copied from shared directories)

Restoring Multisite Backups

Network Restoration

Full Network Restore Process:

Preparation:
- Create fresh WordPress installation (if complete rebuild)
- Or use existing network (if rolling back)
- Ensure database access and file permissions
Restore Database:
- Drop all existing tables (if fresh install)
- Import complete backup SQL file
- Verify table count matches expected
- Check wp_blogs table shows all sites
Restore Files:
- Extract backup ZIP to WordPress root
- Overwrites wp-content with all plugins, themes, uploads
- Ensure wp-config.php has correct database credentials
- Verify .htaccess has multisite rewrites
Network Configuration:
- Update wp_options > siteurl and home (for main site)
- Update wp_blogs > domain column if domain changed
- Regenerate .htaccess if using permalink structure
- Network activate essential plugins
Verification:
- Visit main site – should load correctly
- Visit each subsite – verify content appears
- Test user logins (network admin and site admins)
- Check uploads – images should display
- Verify plugins and themes active correctly

Time Required:

Small network (2-5 sites): 15-30 minutes
Medium network (6-20 sites): 30-60 minutes
Large network (20+ sites): 1-3 hours

Individual Site Restoration

Restoring Single Subsite from Backup:

Scenario: Restore site ID 3 without affecting other sites.

Process:

Backup Current State First:
- Create fresh network backup before restoration
- Safety net in case restoration goes wrong
Drop Site-Specific Tables:
- In phpMyAdmin, drop all wp_3_* tables
- Leaves other sites untouched
Import Site Backup:
- Import SQL file containing wp_3_* tables
- Skip shared and network tables (already exist)
- Or allow overwrites if including shared tables
Restore Site Uploads:
- Delete /wp-content/uploads/sites/3/
- Extract/upload backed up uploads folder
Verify Site ID in Database:
- Check wp_blogs table has entry for site ID 3
- Domain and path should match expected values
Test Restored Site:
- Visit site URL
- Verify content, media, menus display correctly
- Test user logins for that site
- Check other sites still work normally

Challenges:

Must ensure site ID stays same (critical for uploads path)
Shared user accounts may conflict if importing wp_users
Plugin/theme versions may differ from backup time

Restoring to Different Network

Migration Scenario: Extract single site from network, restore as standalone WordPress site.

Steps:

Prepare Standalone WordPress:
- Install fresh WordPress (single site, not multisite)
- Create database
Database Preparation:
- Import site-specific tables (wp_X_*)
- Rename tables to remove site ID prefix:
  - wp_3_posts → wp_posts
  - wp_3_options → wp_options
  - Etc.
- Import user tables (wp_users, wp_usermeta)
Update Site URLs:
- In wp_options table:
  - Update siteurl to new domain
  - Update home to new domain
- Run search-replace on database for old URLs
Restore Uploads:
- Extract from /uploads/sites/X/ (multisite structure)
- Place in /uploads/ (single site structure)
Install Plugins and Themes:
- Manually install plugins that were active on subsite
- Install theme that was active
Verification:
- Site should function as standalone WordPress
- All content, media, users present

Tools to Help:

WP-CLI for search-replace
Search Replace DB script
Backup Copilot Pro’s restore feature (if supports single-site extraction)

Special Considerations

Super Admin Privileges

Backup Permissions:

Only Super Admins can access network-wide backup functions
Site Admins may have site-specific backup capability (if enabled)
Control access via Backup Copilot Pro settings

Security:

Network backups contain all user data across all sites
Encrypt backups if storing offsite
Limit download access to trusted administrators

Domain Mapping

Custom Domains Per Site: If using domain mapping plugin (e.g., brand1.com points to subsite 2):

Backup Considerations:

Domain mappings stored in database (wp_domain_mapping or similar)
Must include domain mapping tables in backup
Document which domains map to which site IDs

Restoration:

Restore domain mapping plugin
Re-import domain mapping tables
Update DNS to point to new server (if migrating)
Test each custom domain loads correctly

Storage Requirements

Calculating Network Backup Size:

Example 20-site network:

WordPress core: 50 MB (shared)
Plugins: 200 MB (shared)
Themes: 100 MB (shared)
Main site uploads: 2 GB
19 subsites uploads (avg 500 MB each): 9.5 GB
Database (all sites): 500 MB
Total: ~12.35 GB per backup

With Retention Policy:

Weekly full: 8 backups × 12.35 GB = ~99 GB
Daily database: 30 backups × 500 MB = ~15 GB
Total storage needed: ~114 GB

Storage Optimization:

Exclude development/test sites from backups
Use database-only backups for daily snapshots
Implement aggressive retention for high-frequency backups

Best Practices

Retention for Large Networks:

Full backups: 4-8 weeks retention
Database backups: 30-day retention
Site-specific: 2-4 weeks retention
Adjust based on storage budget and compliance needs

Monitoring Network Backups:

Set up email notifications for backup failures
Review backup logs weekly
Monitor cloud storage usage monthly
Test restoration quarterly on staging network

Testing Subsite Restores:

Create staging copy of network
Test restoring individual site backup
Verify data integrity and functionality
Document restoration procedure for team

Related Resources

Managing a WordPress network? Backup Copilot Pro offers full multisite support with site-specific backups, network restoration, and automated scheduling for each subsite!