The market had been trying to negotiate a short-term lease extension while considering a possible relocation west of the Hudson River.
The agreement requires Hunts Point Terminal Produce Cooperative to negotiate exclusively with the City for the next nine months in hopes of coming to a long-term solution.
"Our Administration and the Co-op both want that to be built in the Bronx, and in the coming months, we will continue working together to make it happen," Mayor Michael Bloomberg said in a written statement.
Hunts Point first opened in 1967. Its members have been seeking to build a larger, more efficient and modern facility better-suited for refrigeration.