WordPress Multisite: Running From A Subdirectory

Installing WordPress in a subdirectory keeps your site root cleaner and makes it easier to manage core files separately from content. Here’s how to configure WordPress so the admin and core files live in /wordpress while the site appears at your domain root.

Creating the Subdirectory Structure

First, create the WordPress directory and set proper permissions:

mkdir -p /var/www/html/wordpress
chown www-data:www-data /var/www/html/wordpress
chmod 755 /var/www/html/wordpress

Use www-data (Debian/Ubuntu) or apache (RHEL/CentOS) depending on your web server user. Verify with ps aux | grep -E 'apache|nginx|www-data'.

Configuring WordPress Settings

Before moving files, update WordPress configuration in the admin panel:

Log in to WordPress at its current location
Navigate to Settings → General
Set WordPress Address (URL) to https://example.com/wordpress
Set Site Address (URL) to https://example.com
Click Save Changes

You may see a 404 error after saving—this is expected. Don’t attempt to access the site yet.

Moving Core Files

Move all WordPress core files (except index.php and .htaccess) to the subdirectory:

cd /var/www/html
# Move all WordPress files except index.php and .htaccess
rsync -av --exclude='index.php' --exclude='.htaccess' --exclude='wp-content' /wordpress/ /wordpress/
# Or manually move wp-admin, wp-includes, wp-config.php, etc.
mv wp-admin /wordpress/
mv wp-includes /wordpress/
mv wp-config.php /wordpress/
# Move other core files but keep wp-content at root if desired

If you want to serve wp-content from the subdirectory instead, move it:

mv /var/www/html/wp-content /var/www/html/wordpress/

Then add to wp-config.php:

define('WP_CONTENT_DIR', dirname(__FILE__) . '/wordpress/wp-content');
define('WP_CONTENT_URL', 'https://example.com/wordpress/wp-content');

Updating Root Files

Copy .htaccess and index.php from the subdirectory to the root:

cp /var/www/html/wordpress/index.php /var/www/html/index.php
cp /var/www/html/wordpress/.htaccess /var/www/html/.htaccess

If you’re using Nginx instead of Apache, you don’t have .htaccess—configure rewrites in your server block instead.

Modifying Root index.php

Edit /var/www/html/index.php and change the require statement:

<?php
/**
 * Front to the WordPress application. This file doesn't do anything, but loads
 * wp-blog-header.php which does and tells WordPress to load the theme.
 */

/**
 * Tells WordPress to load the WordPress theme and output it.
 */
require( dirname( __FILE__ ) . '/wordpress/wp-blog-header.php' );

Updating .htaccess for Pretty Permalinks

If using pretty permalinks, your root .htaccess needs rewrite rules:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

After moving files, log in at https://example.com/wordpress/wp-admin/ and go to Settings → Permalinks. WordPress will attempt to update the .htaccess file automatically. If you see “Update .htaccess” message, copy the displayed rules manually into your root .htaccess.

Nginx Configuration

If using Nginx, add this to your server block:

location / {
    try_files $uri $uri/ /index.php?$args;
}

location ~ \.php$ {
    fastcgi_pass unix:/run/php/php-fpm.sock;
    fastcgi_index index.php;
    include fastcgi_params;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
}

Reload Nginx:

nginx -t && systemctl reload nginx

Troubleshooting

File permissions errors: Ensure the web server user owns all WordPress files:

chown -R www-data:www-data /var/www/html/

404 on subpages: Verify .htaccess is present and mod_rewrite is enabled:

a2enmod rewrite
systemctl reload apache2

Admin pages not found: Check that wp-config.php is in /wordpress/ and references are correct. Verify the WP_HOME and WP_SITEURL constants aren’t set in wp-config.php (they should be set via the admin panel).

Uploads broken: If wp-content moved to the subdirectory, ensure WP_CONTENT_URL constant is properly defined and the uploads directory is writable.

Your site should now be fully functional with WordPress core files in a subdirectory while the public site loads from the domain root.

WordPress Multisite: Running from a Subdirectory