SAN FRANCISCO—Catholic Charities of San Francisco is still open. The century-old organization is offering free meals for seniors, conducting outreach to the city’s homeless and running two residential-care facilities.

But the revenue streams that usually subsidize those programs, such as youth camps, athletic leagues and transportation services, have been deemed nonessential by the local government amid the coronavirus pandemic and ordered to close. As a result, Catholic Charities projects it will run a deficit of at least $3.5 million by June.

“I don’t know how long we’ll be able to keep serving those vulnerable people,” said Jilma Meneses, the organization’s chief executive.

The coronavirus outbreak is ravaging nonprofit organizations’ finances, threatening many of their usual revenue sources at a time when demand for their services is skyrocketing.