Using Cloudflare on server that has custom nameservers?

I have a website, domain.com, with a server hostname of server.domain.com

The domain.com website is used as a website, as is a few seperate sites like website1.com, website2.com and website3.com.

The other websites are using cloudflare to mask the server’s IP address and make use of Cloudflare’s other benefits.

What I would like to do, is make the domain.com website also protected by cloudflare. If it was a seperate site, that’s easy, but my concern with setting up cloudflare or a similar service would be how it works with the server.

Will my server hostname, AutoSSL, or any of the other features that use the domain.com (https://domain.com) or the server.domain.com (https://server.domain.com) hostname break because I would use cloudflare on the ‘root’ website? When setting up custom nameservers for the first time on domain.com, I have to provide certain information to my domain registrar, but wouldn’t these be erased by changing my domain.com nameserves to cloudflare ones, stopping me from using my custom nameservers on any future domains I add to WHM where I don’t want to use cloudflare? Are there any other risks for applying this change to my main server’s domain?

Thank you for any help.

Cloudflare starts off as plain DNS. Any DNS record set to :orange: will proxy through Cloudflare’s edge servers. As long as your setup is tolerant of using a third party for DNS records, then you’ll be fine.

For example, it sounds like you have ns1.example.com and ns2.example.com name servers. You can have those IP addresses in Cloudflare DNS for example.com and set them to :grey:. Then you can continue to use your ns1 and ns2 name servers as they currently are.

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