Dynamo struggled for the first-half of Kaiser's first season in charge, with the team generally performing well, but unable to convert this into goals. Things picked up in the second half of the season, though, and the team finished in a respectable position in the top half of the 3. Liga table. However, the following season also started badly, and in October, with six defeats in the first twelve games, Dynamo found themselves in the relegation zone, and Kaiser was sacked.
In April 2010 Kaiser signed a two-year contract with Regionalliga Nord side 1. FC Magdeburg, taking over managing duties on 1 July 2010. He is the first foreign manager at the club and is tasked with building a squad that is capable of winning promotion in the 2011-2012 season. However, after a string of bad results brought the side dangerously close to relegation, Kaiser was let go on 17 March 2011, to be succeeded by Wolfgang Sandhowe. After being technical director of Lierse SK for two years, Kaiser returned to a managerial role by signing with Eerste Divisie side FC Den Bosch from July 2013.