Scrubb began 2021 with Houston, but also spent time with the Sugar Land Skeeters with whom he pitched 15 innings. Scrubb pitched a total of 19+2⁄3 innings with the Astros, going 1-1 with a 5.03 ERA and 21 strikeouts. On August 10, 2021, he was placed on the 60-day injured list with a right shoulder strain. On November 30, Scrubb was designated for assignment and outrighted to the Skeeters.