Starting off his career with IFK Timrå in 1998, he went on to represent GIF Sundsvall, AIK, Odd Greenland, 1899 Hoffenheim, and 1.

[1] Following his debut against IFK Norrköping he quickly established himself as a regular central defender, however a series of manager changes and other events made Per feel that he could not perform at top level.

[3] It was widely expected that he would leave for a bigger club,[4] however no bids came until 13 July 2007 when it was announced that Nilsson signed a contract with 2.

[6][7] On 23 March 2014, the Danish club FC Copenhagen announced that they had signed Nilsson on a three-year contract.

[9] In January 2017, RB Leipzig announced that Nilsson would be the assistant to sporting director Ralf Rangnick for the 2017/18 season.