Lowery was booked on charges of assault with a deadly weapon and resisting and delaying a peace officer. He was also wanted on an outstanding warrant.
Lowery is alleged to have stabbed a 46-year-old male volunteer at the church about 10 a.m. Monday. He then reportedly fled on a Muni bus and was arrested by police at Sixth and Market streets.
The victim was stabbed in the shoulder and taken to the hospital for treatment. The injury was not life-threatening.
It was the third reported stabbing in San Francisco since Saturday.