Both churches targeted were in Woodside.
The suspect is accused of stealing computers and dozens of Visa gift cards from the 7th Day Adventist Community Church just after midnight two weeks ago.
He spent hours breaking into a church safe, not realizing it was all being captured on video.
The suspect, described as an adult male in his 30s with a medium build, actually borrowed tools from a storeroom in order to do the deed.
He spent three hours cracking open the pastor's safe to steal the more than two dozen Visa cards, which the church congregation had put together for victims of Superstorm Sandy.
At one point, the man figured out he'd been on camera. So he wrapped a towel around his head and started yanking wires from an electrical closet, hoping to disable the system.
It didn't work, and he ended up staring directly into the camera.
Still, church members say they actually feel sorry for him.
"Nobody's been angry, we feel sorry for him," officer manager Iris Szoboszlai said. "Because if we can get him, he's going to be in jai. And that's worse for him. Instead of coming in here and saying I need help."
Police say the same man also stole electronics and cash from the Sure Foundation Lutheran Church last week.
In both cases, the suspect forced open doors to gain access to the locations.
No one was injured as a result of these incidents.
In the first incident, he was wearing a red baseball hat, a red waist-length jacket, blue jeans and sneakers.
Anyone with information in regards to these incidents is asked to call Crime Stoppers at 1-800-577-TIPS (8477).