On December 10, 2020, the New York Yankees selected Krook from the Rays in the minor league phase of the Rule 5 draft. He began the 2021 season with the Double-A Somerset Patriots and was promoted to the Triple-A Scranton/Wilkes-Barre RailRiders during the season. He started for Scranton/Wilkes-Barre on Opening Day of the 2022 season. Krook had a 10–7 record and a 4.09 ERA for the RailRiders in 2022. His 155 strikeouts set a new franchise record for a season which was previously held by Carlton Loewer since 1997."Klutch: Matt Krook sets franchise record in crucial win," Scranton/Wilkes-Barre RailRiders, Sunday, September 25, 2022. Retrieved January 16, 2023.
