His first game after signing for the club on a permanent basis came on 6 July 2019 against Zenit Saint Petersburg in the Russian Super Cup, as he set up Lokomotiv Moscow's second goal of the game in a 3–2 win. Krychowiak's performance saw him being named the club's Player of the Month in the first three months to the season. After missing two matches due to suspension and injury, Krychowiak returned to the first team in a 3–0 loss against Spartak Moscow on 27 October 2019. Two weeks later, in a match against FC Krasnodar on 10 November 2019, Krychowiak suffered an injury that saw him substituted at half time. After the match, it was revealed that he suffered a concussion, but quickly recovered. He scored twice in a follow-up match, in a 3–2 win against Tambov. As a result, Krychowiak was named Lokomotiv Moscow's Player of the Month for November. Following this, he remained in the first team until the season was suspended because of the COVID-19 pandemic in Russia. In the league's last match before the suspension, he scored his 10th goal of the season in a 3–1 win against Rostov. Following this, Krychowiak was named the club's Player of the Month for March. He remained an integral part of the team once the season resumed behind closed doors and made six further appearances, helping Lokomotiv Moscow qualify for the UEFA Champions League next season.