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There's this "Site Icon" option in the customizer, which allows you to set a favicon. I'm creating a theme which already has its own favicon.

How can I check if the favicon is already set in the customizer?

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WordPress saves the Favicon as site_icon in the options table holding the attachment post ID. What you could do is something like this:

if( false === get_option( 'site_icon', false ) ) {
    // Show favicon
}

Where get_option() will hit the default ( we provide as the 2nd parameter ) false IF the site_icon does not exist or one has not been uploaded through the customizer.

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