In 1994, he began his coaching career as a youth coach for Legia Warszawa. He managed SMS Piaseczno during the 1998–99 season. From 1999 to 2003, he coached the Amica Wronkiyouth team and was successful in winning a league title in 2002. He also was an assistant to Mirosław Jabłoński while at Wisła Płock. In May 2003, Paweł Janas appointed Skorża as an assistant coach for the Poland national football team. However, following Poland's elimination from the 2006 FIFA World Cup group stage, entire of the staff, including Maciej himself, was sacked by the Polish Football Association. He had a short spell at Wisła Płock as an assistant manager before returning to Amica Wronki as manager in 2004. In the 2004–05 season, Skorża became the first Polish coach to manage to qualify a Polish football club to the group stage of the UEFA Cup. In the 2006–2007 season, he joined Dyskobolia Grodzisk Wielkopolski and won the Polish Cup and Ekstraklasa Cup. On 13 June 2007 Skorża was appointed as the manager of Wisła Kraków which he led twice to league title, winning Ekstraklasa in seasons 2007–08 and 2008–09. He worked with Wisła Kraków until 15 March 2010, when the Wisła'sboard of directors fired him after a series of three games without a win, in spite of the club holding the lead of the league. On 1 June he was announced as the new manager of Legia Warszawa. On 30 May 2012, Skorża's two-year spell as Legia warszawa manager came to an end. On 1 September, Skorża was appointed as the new manager of Lech Poznań, signing a three-year contract with the club. Skorża after draw against Wisła Cracow on 7 June won Polish Ekstraklasa in the first season working in Poznań and celebrated his third Polish champion title in manager career. This game was watched by 42000 of fans from the stand, the highest attendance of whole 2014/2015 season in Poland. Starting the next 2015/2016 games Skorża played in Poznań with Legia Warsaw for the Polish SuperCup. His Lech won the trophy after great victory 3:1 over most dangerous rival. This game watched 40000 of viewers and was beaten record of the SuperCup's competition audience size.