On November 15, 2019, Stewart-Haas Racing announced that Custer will replace Suárez in the No. 41 Ford in 2020. On December 4, Stewart-Haas Racing announced that Mike Shiplett will replace Billy Scott as the crew chief of the No. 41 team. Both Shiplett and Custer worked together during the 2019 NASCAR Xfinity Series. After just collecting a top ten finish in the first 16 races, Custer finished 5th at Indianapolis, his first career top five and the team's best run at that point. With 1 lap to go at the Quaker State 400 at Kentucky Speedway the following week later, Custer slipped by Ryan Blaney, Kevin Harvick, and Martin Truex Jr. in an incredible four-wide pass for the lead to cruise to his first career victory. Custer became the first driver to score their first career win with the team. His win earned him a spot in the 2020 Playoffs, but he was eliminated after the Round of 16 at Bristol.