You should be able to add a rewrite condition to prevent WordPress from taking over the URLs for tracker: RewriteCond %{REQUEST_URI} !tracker/
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_URI} !tracker/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !tracker/
RewriteRule . /index.php [L]
</IfModule>
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteRule ^wp-admin/profile\.php$ /ssm/welcome [R]
</IfModule>