Since there isn’t a way in Cpanel to actually disable the email service, you can remove the ability from Cpanel that allows it to send email directly. Basically there are two files that need to be editted. The remotedomains and the remotedomains file. In the localdomains, it includes every domain that has been setup in cpanel. What you need to do is access that file and remove that entry from it. So if you were to log into the server, you would shell in and perform this. An example would be like;
#vi /etc/localdomains
In the file you would see a listing like this;
:localhost
:Mydomain.com
:Myhost.com
So if you wanted to disable mail for Mydomain.com, you would simply remove it and save it. Then you would edit the remotedomain file;
# vi /etc/remotedomains
And then add the domain you removed from the localdomain to here. Save the file and restart the mail services. That’s it.
This is also helpful if you are hosting email external and Cpanel is ignoring the remote / external MX records.
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