You might say: "The user does an action. Next, he cooks lunch." Saying "The user does an action. Next, it cooks lunch" is odd.
A common workaround is to use "they" as a 3rd person gender neutral singular pronoun. "The user does an action, Next they cooks lunch." But this is even more odd and confusing, since they is a 3rd person plural pronoun. So you have to alter the verb to match, and you get "The user does an action. Next, they cook lunch." This is turn can change the meaning of your sentence, because you really don't mean 2 or more users. You are talking about a single user.
I have always struggled with this myself and am never really sure what to do. My default is to alternate between "he" and "she"