The £100m scheme includes a new ground for non-league Boston United, along with shops and 500 homes in the Wyberton area of the town.
Wyberton Parish Council held the vote after residents called for it.
Of those eligible to vote, only 18.76% - 550 people - took part, of which 86% voted against the scheme.
Parish council chairman Richard Austin said: "I wasn't expecting a big turnout, but I'm sure the World Cup game had an effect."
He said the date and time had been "set in stone" and the council could not change them.
However, he added: "I can only speculate, but perhaps the majority were happy to take the view of the ones that did vote.
"We live in a democratic society and this is what happens sometimes."
Mr Austin said prior to the vote people had raised concerns over the potential impact of the scheme, including the traffic it would generate.
He said the parish council would now consider the results before forming its view on the application to Boston Borough Council.
The developer, Chestnut Homes, whose owner David Newton is Boston United chairman, said the project would be good for the town and create jobs.
The project, called The Quadrant, includes plans to move the Conference North club from its York Road stadium, where it has been since the late 19th Century, to a new 4,000-seat ground off the A16 at Tytton Lane.
Chestnut Homes submitted its planning application in May. If approved, work could begin in 2015.
England's game against Uruguay has been partly blamed for a low turnout in a referendum on plans to build a football stadium and new homes in Lincolnshire.