On 30 June 2009, it was confirmed that Bristol City had completed the signing of Gerken for an undisclosed fee, to end his seven-season stay with Colchester United.

Gerken was arrested on suspicion of indecent exposure in the early hours of 25 October 2009 after he was allegedly spotted urinating in public.

Soon after he joined Ipswich he replaced Scott Loach as the first choice goalkeeper, starting 41 league games in his debut season at the club, keeping 10 clean sheets.

[19] However, with the arrival of fellow keeper Bartosz Białkowski in 2014, Gerken's first team play time would decrease gradually.

[23][24] Following his release by Ipswich Town, Gerken re-signed for his first club Colchester United on 13 July 2019 on a free transfer.

[26] On 24 January 2020, Gerken made his 300th career appearance in a league match against Bradford City, which ended in a 0–0 draw.

[29] In July 2023, in addition to his role with the Championship club, he joined National League South side Bath City as goalkeeping coach.