Michael Jones was accused of religious harassment concerning allegations he preached about homosexuality and abortion, however, the charges were dropped by the Crown Prosecution Service.
The 66 year old from Hornsea was arrested at his home in December 2015 and spent the day in police cell.
The payment he has received is understood to form part of an out-of-court settlement.
Residents from Beverley, where the evangelist works part-time, reportedly started a petition to try and get him barred from the area.
Mr Jones tolds the Scunthorpe Telegraph: "A week ago they rang me and said they were providing me with £3,000 in compensation. But they are still holding my DNA, fingerprints and photograph and I don't think that's right.
"It's not about the money, really. I don't care that much about the money although it is very handy and I will be giving some of it away to various charities.
"I'm pleased. I have had no trouble with the police before or since and I'm still out there."
Humberside Police was reported as saying it civil matter and so it could not comment.