He could operate as either a left-back or a central defender, and played solely for Bayern Munich, winning ten major titles and appearing in nearly 400 official games.
After two experimental seasons he became first-choice, scoring a total of 27 Bundesliga goals from 1983 to 1988 and playing all the matches and minutes in the 1986–87 European Cup, as the team finally finished second to FC Porto.
However, a flood of injuries to the side in 1995 prompted a request by manager Giovanni Trapattoni which the player accepted, appearing on 8 April in a home game against 1.
FC Kaiserslautern where he was also booked; even more astonishingly, he spent the entire 2001–02 with the B team in Regionalliga Süd, helping them to a final tenth place at the age of 42.
Pflügler was also picked for the 1990 FIFA World Cup as Andreas Brehme's backup, playing 90 minutes of the 1–1 group-stage draw against Colombia for the eventual champions.