On 29 September 2021, after Mroczkowski's dismissal, Kroczek took on the role of manager,[3] which he held until the end of the season, which Resovia finished in 11th.[4]
On 27 June 2022, he returned to III liga to manage Unia Skierniewice;[5] with Kroczek in charge, Unia finished the season 7th in their group, with a record of 15 wins, 8 draws and 11 losses. He left the club by mutual consent one year and a day after his appointment.[6]
In February 2024, he joined Cracovia as a head of methodology department for youth teams, and was due to take charge of Cracovia's reserve side from the start of the 2024–25 season.[7] However, after Jacek Zieliński's sacking following a 2–2 league draw against ŁKS Łódź on 5 April 2024, Kroczek was promoted to the role of interim manager until the end of the campaign.[8] His first game in charge on 14 April ended in an upset 1–3 away win over league leaders Jagiellonia Białystok.[9] On 23 May 2024, the club announced that Kroczek had signed a contract to become a full-time manager of Cracovia until 30 June 2025, with an option for a further year.[10]