He made his debut for the club in a 0–0 draw against Spartak Moscow on 4 August 2018. Two weeks later on 19 August 2018, Krychowiak scored his first goal for Lokomotiv Moscow, in a 1–0 win against Krylia Sovetov Samara. This was followed up by setting up three assists in the next three matches, in which he was sent off for a second bookable offence against Dynamo Moscow. For his performance, Krychowiak was named the club's Player of the Month for August and then for November. He captained Lokomotiv Moscow for the first time in his career against Yenisey Krasnoyarsk in the round of 16 of the Russian Cup, only to receive a straight red card in the 71st minute, as the club won 4–1 to advance to the next round. Since joining Lokomotiv Moscow, Krychowiak established himself in the first team, playing in different midfield positions, and also rotated playing in the centre-back position. On 10 May 2019, Krychowiak scored his second goal of the season, in a 4–0 win against Rubin Kazan. He then started in the centre-back position in the Russian Cup Final against Ural Yekaterinburg and helped the club win 1–0 to win the tournament. Following this, Krychowiak said the season was successful, having helped Lokomotiv Moscow finished second place in the league and winning the Russian Cup. At the end of the 2018–19 season, he went on to make 39 appearances and scoring two times in all competitions.