The Winnipeg Blue Bombers named Walters interim General Manager for the remainder of the 2013 CFL season following a disappointing 1–5 start. The team didn't finish any better, going 2-10 the rest of the way and failing to qualify for the CFL playoffs. Despite the disappointing finish to the year, the Bombers removed the interim tag and named Walters GM for the 2014 CFL season. In 2014 the Bombers finished 7-11 following a 5–1 start. In the offseason Walters made some key signings for the offensive line, including Stanley Bryant and Jermarcus Hardrick.
Walters helped to build to foundation of a successful Blue Bombers team that saw them have four consecutive double-digit win seasons in 2019. The team carried this success into the 107th Grey Cup which they won over the Hamilton Tiger-Cats 33–12. Due to the championship caliber team he had built, the Bombers extended his contract in 2019 through to the 2023 season.[3] Walters prefers to do the scouting for the team and work in the background, while Mike O'Shea does most of the media interviews for the team.[4] O'Shea was also extended at the same time, though his contract ends one year earlier in 2022.