Pastor Jack Trieber from a Santa Clara at North Valley Baptist Church was fined $15,000 for defying the restraining order by Gov. Gavin Newsome.
Trieber repeatedly disobeyed orders designed to limit the spread of the disease, causing significant public health and safety concerns.
Over the weekend and on Wednesday, Trieber led indoor services and singing, which state health officials say "likely increase the risk of transmission of the virus."
Trieber was fined $5,000 twice over the weekend and was fined another $5,000 on Wednesday.
Trieber was aware of the restraining order to protect members of the public from coronavirus and argued in a video that his parishioners kept the social distancing and wore masks.
The freedom of expression and worship was mentioned in his video as well. "Absolutely, we have a First Amendment right, you can't make laws against the church, we have the right to worship," said Trieber.
He also used the county's death rate to justify indoor services in his nine-minute video.
"He's using the somewhat low numbers in Santa Clara County, which are the sign of success of their policies, to violate the policies and that's not very good," said Dr. Steven Goodman, Stanford University professor of epidemiology and associate dean of the school of medicine.
Officials said the church's ability to spread the disease is particularly concerning, and churches have been warned on numerous occasions not hold any indoor services.
The lawsuit was filed against Pastor Jack Trieber and his church. No incidents or arrests were reported.