SAN JOSE — A vacant former Nob Hill grocery store at the center of a debate over whether the city should step in when commercial landlords let empty storefronts fester will soon become a church.

But community leaders who protested other plans to fill the site that had become blighted and infested with rodents over the last two years said the latest proposal is hardly an improvement for the struggling retail center.

“I was disappointed. I think it’s inappropriate for a church to be inside an anchor store in a strip mall,” said Issa Ajlouny, who has lived in the neighborhood for 33 years and spearheaded a push to get the space filled. He fears the church will attract homeless people to the shopping center.

“Will that make things worse?” Ajlouny asked. “Is that fair to the other stores in the center?”

Pastor Micaiah Irmler of the Southridge Church was unavailable for comment.

The dispute over the site began after Nob Hill closed its doors two years ago, but renewed its lease for the vacant building at 7076 Santa Teresa Boulevard. Nob Hill representatives said they closed the store because of slumping sales but maintained the lease to explore opening a distribution center there. That plan didn’t pan out.

Residents opposed a plan to open a gym or a Nob Hill Express inside the vacant store, arguing those would not help reactivate the center, which is home to several restaurants, a Goodwill store, a bargain dollar store and an auto parts retailer.

“We didn’t think a Nob Hill Express was a viable option for them, because they said they couldn’t make money on it,” said John Levstek, a telecom professional who’s lived in the neighborhood for nine years.

Meanwhile, the darkened store attracted homeless people, trash and rodents — triggering outrage from neighbors and pitting the grocer against its landlord.

Officials from Retail Opportunity Investments Corp., which manages the shopping center, said their hands were tied — Nob Hill had the option to renew its lease and their contract did not have a termination clause.

The two companies pointed fingers during a public meeting two months ago as community pressure mounted.

But last week, Nob Hill leaders announced they found someone to sublease the space — Southridge, a new Baptist church that’s been using the Southside Community Center on Cottle Road as its temporary home.

Chelsea Minor, a spokeswoman for Raley’s, which owns Nob Hill, said she believes the church will “activate the space with community services, meeting space and other events.”

“We heard the neighborhood clearly that there was a strong desire to fill the vacant space,” Minor said. “Since that meeting, we have been working to find a subtenant to fill the space. The community asked that the space be activated, and we believe the church will serve the community well.”

But Ajlouny said he and his neighbors wanted to see another retailer.

“It’s a retail strip mall, and the residents want a store to draw people there,” Ajlouny said.

Levstek said he has nothing against places of worship but “this is a retail environment,” and he believes Councilman Sergio Jimenez should’ve fought harder for a new retail store.

Jimenez, who represents the district, acknowledged that a church may not be the “ideal situation,” but said he has no control over who a private company like Nob Hill leases to.

“Having traffic and people there as opposed to having it be vacant is a win,” Jimenez said. “I hope folks understand it’s better than having a vacant storefront, and it’s going to drive traffic for a lot of the businesses. It’s a good result given that it’s been empty for two years.”