Allen signed with Andy Kilner's Stockport County in October 1999, and played sixteen games in 1999–2000. He then signed with Brighton & Hove Albion, but did not make a senior appearance. He spent summer 2001 on trial at Cambridge United, but was not offered a contract. He signed with Dover Athletic in October 2001, after manager Gary Bellamy said that he "destroyed the opposition" in the three games he played on trial. He played 17 Conference games in 2001–02, as the "Whites" finished bottom of the table and were relegated into the Southern League.