He turned in a number of impressive performances for Aris Nikeas playing 21 games.
In the summer 1991 he joined to AO Neapolis having an impressive performances for AO Neapolis playing 24 games.
In the summer 1992 michalis Kapsis signed for the Greek Third Division team called Anagennissi Artas that launched also the legendary goalkeeper Antonis Nikopolidis that will become team mate in winning Euro 2004 with Greece Nazional Team. Here Michalis Kapsis played for 1 season for 18 matches and scoring 1 goals.
The step up in class did not have a negative effect on the player's game, Kapsis amassing 30 appearances - his highest tally ever. In total he scored just one goal in 123 games for the new club. Michalis Kapsis helped Ethnikos Piraeus achieve promotion to the Greek top flight in his first season at the club, 1993/94
During the 1998/99 season, Michalis Kapsis joined AEK. He finished that campaign with 15 AEK appearances under his belt in 1999 and was a regular over the next two seasons before, in 2001/02, he was fined for his involvement in a training ground row with goalkeeper Elias Atmatsidis, as AEK surrendered the championship to Olympiacos CFP in the closing weeks of the season. In 2002/03, he featured in AEK's six UEFA Champions League draws. It was the first time in Greek football history that both a father and his son had participated in the top European clubs' competition; his father Anthimos had been playing for Panathinaikos in the Champions' Cup during the 70's (the two were followed some years later by Celtic's Georgios Samaras, son of Ioannis). He also played 20 Alpha Ethniki games. Kapsis was his usual consistent self in what was a disappointing 2003/04 campaign for AEK, who finished fifth. Fine performances earned him a call-up for the critical UEFA EURO 2004 qualifying matches against Spain and Ukraine; he marked Raúl González and Andriy Shevchenko superbly in famous victories. He was also ever-present in the wonderful run in Euro 2004 that gave Greece the European title, and remained a regular in FIFA World Cup qualifying.
After EURO 2004, he left AEK and signed for FC Girondins de Bordeaux. He played 29 league matches in France,. After this performance many club made an offer to Michalis Kapsis for a possible new contract.
In the summer 2005 he signed two-year deal with champions Olympiacos. He has since failed to settle at the Piraeus club. Frequent injuries and a lack of confidence from successive coaches have deprived him of a first-team slot. There was often speculation about his future at the club, and he was allegedly offered as an exchange in a failed transfer bid for PAOK's Dimitris Salpingidis. Trond Sollied announced on 31 August 2006 that Kapsis would not be included in the team eligible to participate in the 2006-7 UEFA Champions League competition.
Michalis in February 2007 moved to APOEL in Nicosia, Cyprus and helped the club win the champion title race for 2007. The agreement was for that season only with the option to renew for the next one. Kapsis renewed, extremely pleased with the club. In August 2007 PAOK FC chairman Theodoros Zagorakis was interested in bringing him to PAOK. Kapsis said that is proud of PAOK's interest, but is also under a contract at APOEL and will honor this. At the end of the season he won the 2008 Cypriot Cup with APOEL.
In July 2008 he signed a 2-year contract with the minor Super League side of Levadiakos. Michalis Kapsis made his debut for Levadiakos in the Super League on 31 August 2008 against Aris Thessaloniki at the Harilaou Stadium in Thessaloniki. Michalis Kapsis heped the team during the season 2008-2009 to do not be relegate in the second division becoming one of the most important player with experience for the new team. He played the first match of season 2009/2010 against Kavala FC, where the goalkeeper Fanis Katergiannakis and the midfield Vassilios Lakis played.
In February 2010 Michalis Kapsis signed for Ethnikos Piraeus, expressing his desire to play for the team where he debuted as a professional player before retiring.
Michalis Kapsis was included in the squad of Euro 2004 that ended up winning the tournament and in particular Kapsis achieved a great performance. Kapsis was included in the Greek squad for the 2005 FIFA Confederations Cup in Germany. Otto Rehhagel also included him in the squad for the qualifying rounds to the UEFA Euro 2008 in Switzerland and Austria. Michalis Kapsis made 34 appearances and even scored a goal against Georgia for FIFA World Cup qualification 2006 on 26 March 2005 in Georgia where Greece won 1–3.
Ethnikos PiraeusGreek Second Division: 1994
Greek Second Division: 1998
AEK AthensGreek Cup: 2000, 2002
OlympiacosGreek Championship: 2006
Greek Cup: 2006
APOELCypriot Championship: 2007
Cypriot Cup: 2008
GreeceEuropean Championship: 2004