A noun phrase headed by way — that is, the noun way plus any adjectives, determiners, relative clauses, etc. — can be used adverbially. For example:
He did it the way she asked.
Either way, we're out of time.
Look both ways before crossing the street.
She came in through the back door, and left the same way.
So although it's fine to use in in your example, it's also completely fine to leave it out. (Personally, I think it sounds better without the in.)
Way is rather unusual in this respect, but not absolutely unique. The same happens with many nouns relating to time:
They go to church every week that they're in town.
She tried it three times before giving up.
He's moving away next month.