It took me a while to find the answer to how to deactivate Genesis SEO and replace with WordPress SEO by Yoast. The answer is a simple one:
Just install WordPress SEO by Yoast.
That’s it. Genesis Framework has built in a check for WordPress SEO by Yoast plugin (amongst a number of others SEO plugins) and once identified Genesis SEO and it’s settings is deactivated essentially replacing the Genesis SEO tools with the new plugin.

Yoast has a Genesis Theme Review in which they confirm:
As soon as you enable my WordPress SEO plugin, Genesis hides all of its SEO settings and lets WordPress SEO run the SEO show.
* Note: replacing the Genesis SEO tools with WordPress SEO by Yoast isn’t a judgement on the quality and effectiveness of Genesis SEO. It’s mostly an issue of portability for me. There is a syncing ability, but for me, and for a new installation, I prefer just sticking with the plugin I’m more familiar with.
References:
To replace Genesis SEO with Yoast SEO Plugin simply install and activate the Yoast SEO Plugin. This will be detected and Genesis SEO will be deactivated.
- Genesis Theme Review by Yoast (see: “Compatibility with WordPress SEO”)
- Ultimate SEO and Genesis