José Alvarrado saved for more than a decade to buy 3 Brothers Mini Market, a bodega at 169th Street and Audubon Avenue.

But at his store on a recent weekday morning, only eight months after he opened shop in Washington Heights, shelves that had held bags of rice and beans were empty. Gallons of milk lay sideways in a refrigerated case, offered at half-price or less.

Mr. Alvarrado is closing his store, saying that even with a five-year lease, rising rent and other conditions make it impossible to stay.

His situation is similar to one faced by many bodega owners throughout Upper Manhattan: Despite their profitability, stores are being squeezed out of the neighborhoods they call home. Once lonely grocery outposts in a dangerous city, their colorful awnings part of the streetscape, they are now losing customers to chain stores.