Open Mail → Settings → Signatures
In macOS Mail.app, press Cmd + , to open Settings, then click the Signatures tab. Pick the email account you want the signature on (or use the default 'All Signatures' option for an account-agnostic signature). Make sure the box 'Always match my default message font' is unchecked — that box strips the HTML and gives you a plain-text signature instead.
Why this works
Apple Mail stores signatures per email account. If you have 3 mail accounts, you need to add the signature 3 times unless you use the 'All Signatures' option. The 'Always match default font' box is the most common reason a generated HTML signature turns into a plain-text wall of Times New Roman on the recipient's side.

