The Planning Commission preliminarily turned down a proposal to locate a Whole Foods 365 store in the former Lombardi’s sporting goods store at the corner of Polk and Jackson streets by a 5-1 vote Thursday.

After a four-year fight that focused on everything from housing to the impact chain stores have on mom-and-pop businesses, the Planning Commission rejected a stripped-down version of the Whole Foods concept for 1600 Jackson St., which housed Lombardi’s until 2014.

Under the latest version of the plan, the store would have occupied the entire first floor — about half of the 43,900-square-foot building — and half of the second floor, about 11,000 square feet. The rest of the second floor would have contained eight residential units.

The commission had previously asked the developer to include some housing in the project, and several members expressed concern Thursday that eight units were not enough.

Its president Rich Hillis, cast the lone vote in support. The commission will take a formal vote on the project Nov. 29.

But while the project in its current form is probably at a dead end, the commission indicated the developer could approach the site in a different way. Including more housing would require tearing down the current structure and building a new one. But the area’s zoning prohibits commercial spaces larger than 4,000 square feet, not big enough for a full-service grocery store.

It’s possible, though complicated, to change the zoning for a specific site. Known as “spot-zoning,” this could open the possibility of a commercial space big enough for a grocery store topped with additional the housing units both the commission and many public speakers at the hearing said they favored.

The approval process started in 2015 when Whole Foods first proposed opening the store. While grocery stores are typically popular even in neighborhoods that resist chains, a collection of small business owners and some residents opposed the Whole Foods, arguing it would dilute the character of Polk Street’s retail community and hurt long-standing operators such as Cheese Plus and the Jug Shop, a wine and spirits store.

Michael Priolo, owner of the nearby Jug Shop, called the proposed store “a retail killer” during public comment.

But proponents of the plan — which included many immediate neighbors — argued that the neighborhood lacked a full-service grocery store and that the foot traffic generated by the store would help nearby independent stores.

Others opposed to the project, including several commissioners, said the site should be used for housing instead.

“I could not in good conscience let this be a supermarket for the next 25 years in a time of a housing crisis,” Commissioner Milicent Johnson said.

The Planning Commission had delayed a vote several times, asking the property owner, Village Properties, to explore the feasibility of adding some housing units above the store, which resulted in the project presented Thursday.

The commission also voted 5-1 to approve legislation rezoning a roughly 5 acre parcel at 1550 Evans Ave. in the Bayview so the property can become the site of a new and long-awaited community center. The parcel is being used as surplus office space for the San Francisco Public Utilities Commission, which owns the property.

The legislation, which will require the approval of the Board of Supervisors, includes a provision that would allow for below-market-rate housing to be built as part of the community center project. The housing provision was written by President Malia Cohen, who represents the Bayview.

In May, the parcel became a political flash point that exposed tension between the need to build affordable housing in the neighborhood and community autonomy. Many in the Bayview were incensed to learn that, after working with the utilities commission for years to design the community center, city officials were working behind the scenes on an alternative proposal that included about 250 units of affordable housing.

Commissioner Dennis Richards cast the lone dissenting vote, siding with many in the Bayview who believe that the development of 1550 Evans should hew to the plan the community created with the utilities commission.

Commission General Manager Harlan Kelly has repeatedly stated that there are no plans to build housing as part of the 1550 Evans development, which is slated to begin next year.

Dominic Fracassa and J.K. Dineen are San Francisco Chronicle staff writers. Email: dfracassa@sfchronicle.com, jdineen@sfchronicle.com Twitter: @dominicfracassa, @SFjkdineen