In July 2008, he moved to Eintracht Frankfurt for a fee of €900,000. In his second season, he struggled to find a regular spot and announced that it was his intention to transfer. On 29 December 2009, Eintracht Frankfurt loaned him to 1. FC Kaiserslautern until the end of the season. At the end of the season, he returned to Frankfurt but was unable to make an impact. In January 2011 Markus Steinhöfer left the Frankfurt to join FC Basel. He played his first game for his new team on 6 February 2011 in the 3–2 away win against FC Thun. He played all 18 Swiss Super League games and at the end of the 2010–11 season Steinhöfer won the Championship with Basel. On 7 December 2011, during the Champions League group C match at home to Manchester United, trying to make a clearance, Steinhöfer volleyed the ball against his own crossbar. Basel won the match 2–1, sending United out of the Champions league. Steinhöfer's fans created a song to celebrate this feat. Steinhöfer scored his first Super League goal in the 3–0 away win against Sion on 22 April 2012. At the end of the 2011–12 season he won the Double, the League Championship title and the Swiss Cup with the club. At the end of the Swiss Super League season 2012–13 he won the Championship title and was Swiss Cup runner up with Basel. In the 2012–13 UEFA Europa League Basel advanced as far as the semi-finals, there being matched against the reigning UEFA Champions League holders Chelsea, but they were knocked out, losing both home and away ties, beaten 2-5 on aggregate. In a long season with a total of 76 games he had a total of 63 appearances. After two and a half years in Basel his contract was not extended. Subsequently Steinhöfer played for 2. Bundesliga club 1860 Munich. His contract was dissolved on 1 February 2015. Just on the following day he moved to league rivals VfR Aalen, signing a contract until the end of the season. On 17 June 2015, Steinhöfer's signing was announced by Sparta Prague of the Czech Republic. He played there for one season. After that Steinhöfer went to SV Darmstadt 98 that played in the German Bundesliga at this time. For the following season SV Darmstadt 98 was relegated to the 2. Bundesliga. Steinhöfers contract was canceled at the end of 2017/18 season. In September 2018 Steinhöfer signed contract with VfB Eichstätt in Regionalliga Bayern.
