University Christian Church collaborated with County health officials to give the vaccines to churchgoers, homeless people and anyone else who wanted a vaccine.
"This is truly an epidemic that is going on in San Diego and it's just one step that one group of people can do to make it better,” church member Allison Dewse told NBC 7.
A third of the cases involve people who used illicit drugs and are considered homeless. Of the cases, 25 percent are neither homeless nor drug users.
The City has started to install portable bathrooms and handwashing stations in downtown.
Nearly 500 people have been sickened in the epidemic.
A local health emergency was declared on Sept. 1.