On August 1, 2022, the Yankees traded Wesneski to the Chicago Cubs for relief pitcher Scott Effross.[9] The Cubs assigned him to the Iowa Cubs, with whom he was 0-2 with a 5.66 ERA.[10][11][12] The Cubs promoted Wesneski to the major leagues on September 6.[13] He debuted that day and pitched five scoreless innings with eight strikeouts en route to his first career win.[14] On September 22, Wesneski pitched an immaculate inning versus the Pittsburgh Pirates.[15] He finished his rookie campaign with a 2.18 ERA in 6 games.
In 2023, Wesneski made 34 appearances (11 starts) for the Cubs, and registered a 3–5 record and 4.63 ERA with 83 strikeouts across 89+1⁄3 innings pitched.[16] Wesneski was optioned to Triple–A Iowa to begin the 2024 season.[17] He made 28 appearances for Chicago, posting a 3–6 record and 3.86 ERA with 67 strikeouts across 67+2⁄3 innings pitched.[18]
Houston Astros
On December 13, 2024, the Cubs traded Wesneski, Isaac Paredes, and Cam Smith to the Houston Astros in exchange for Kyle Tucker.[19] He made six starts for Houston, logging a 1-3 record and 4.50 ERA with 29 strikeouts across 32 innings pitched. Following a May 6 start against the Milwaukee Brewers, the Astros placed Wesneski on the 15-day injured list with right elbow discomfort.[20] On May 18, it was announced that Wesneski would undergo Tommy John surgery, ruling him out for the rest of the season.[21]
On March 30, 2026, Wesneski was placed on the 60-day injured list as he continued to recover from surgery.[22]