Crystal Dynamics boss Dermot Gallagher has departed the company after a decade at the studio.
Gallagher was also head of product development and Western studios for Square Enix, with responsibility for the publisher's non-Japanese output.
Crystal Dynamics veterans Scot Amos and Ron Rosenberg have stepped up as co-studio heads, with the duo said to have been acting as such for "a few months" already, Square Enix describes the transition as "seamless".
"I want to thank him for his tremendous effort and contribution to Square Enix, along with the amazing entertainment he has helped create," Square Enix Western CEO Phil Rogers commented in a statement.
"I am sad to see him go but respect his decision and we should all celebrate the sheer blood, sweat and tears he has put into our company over the last 10 years!"
Square Enix has released Rise of the Tomb Raider, Lara Croft Go, Just Cause 3, and Life is Strange this year but Gallagher's connection to Tomb Raider will be his enduring legacy.
Rise of the Tomb Raider launched in November on Xbox One and Xbox 360. The game is coming to PC and PlayStation 4 in 2016 with a recent listing suggesting it could be released on PC as early as January.