After struggling with Cambridge United for much of the 2006–07 season, Quinn led them to 17th place, avoiding relegation to the Conference South on the final day of the season. After bringing in Alan Lewer as his new Assistant, he led the U's to an impressive start to the following season, which saw them top the division after an unbeaten start to the season. He also oversaw a Boxing Day victory over local rivals Histon. Mark Albrighton's goal gave them a 1–0 victory at a packed Abbey Stadium, and revenge for the 5–0 thumping Histon gave the U's in the FA Trophy in December 2006.