WordPress sites missing from WordPress Manager
WordPress Manager only lists sites Softaculous installed. Scan for manual installations to bring the rest under management.
A WordPress site exists on your account but does not appear in WordPress Manager by Softaculous. Applies to shared, reseller and Premium hosting.
WordPress Manager only tracks installations it created. Anything installed by hand, restored from a backup, or migrated from another host is invisible to it until you scan.
Import your existing sites
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In cPanel, open WordPress Manager by Softaculous under Software.

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Select Scan.

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Select Manual Installations.

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Select Start scanning for installations.

Your sites appear once the scan finishes.
What this gives you
Sites under management get one-click updates for core, themes and plugins, staging site creation, and cloning between accounts. None of that is available for an installation Softaculous cannot see.
If a site still does not appear
- It is outside your home directory. The scan only covers your own account.
wp-config.phpis missing or unreadable. The scan identifies WordPress by that file; if permissions block it, the installation is skipped.- It is not actually WordPress. A partially restored or broken installation may not be detected.
Re-run the scan after moving or repairing the installation.