Members of Raunds Co-operative Society have rejected a proposal to merge with Midlands Co-op.
Some 171 of Raunds' 4,000 members attended a special general meeting last week to vote on the deal.
Although a majority backed it, the poll fell 14 votes short of the two-thirds majority needed.
Raunds Co-op, which operates a large supermarket, a non-food store and a farm in Northamptonshire, said it would ask its members why they had not backed the merger.
"I would urge them to consider what the future might hold," said Keith Tindall, CEO and secretary of Raunds. "We need a strong partner to withstand competition. Midlands Co-op is a very sound neighbouring society."
Midlands Co-op CEO John Fitzgerald added: "We regret that a small number of members of Raunds chose not to vote in favour, as the prospect of trading co-operatively is logical in such a competitive environment."