A small chain of neighborhood thrift stores in Boston and Cambridge that helped fund HIV prevention and wellness since the mid-1990s will shut down in June.

Fenway Health announced Tuesday the plan to close its Boomerangs stores in Jamaica Plain, the South End and Cambridge's Central Square. The organization said it decided to close the stores because they have been losing money, noting that they used to bring in a few hundred thousand dollars annually but now lose over $500,000 a year.

“Over the years, Boomerangs has raised a lot of money to help support HIV care and services and has had a positive impact on the lives of many people here in Massachusetts,” said Chris Viveiros, Fenway Health's director of communications. “Unfortunately, Boomerangs is dealing with the same challenges that face other brick and mortar retail stores.”

He added that the organization needs to prioritize its health care services, not retail.

“I mean, that's money that could be used to support care and services for our patients and clients,” he said.

Viveiros said Fenway Health will do “whatever we can” to support the roughly 50 people currently employed at the stores.

Customers on social media responded to the news with a mix of sadness and frustration. Some blamed Fenway Health for what they argue was an avoidable outcome. The stores were originally opened by AIDS Action, which merged with Fenway Health in 2013.

“I am sure there are folks in the community who are sad about this,” Viveiros said. “I'm sad about this — I used to shop at Boomerangs all the time when I lived in Jamaica Plain.”