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.

Clare Mackintosh said it was "a dream come true" to see I Let You Go named best crime novel at the Theakston Old Peculier Crime Writing Festival.
She beat five authors, including Robert Galbraith - the crime-writing pseudonym of Harry Potter author JK Rowling.
Author Val McDermid was also honoured with an outstanding contribution award at the festival she helped to set up.
Oxfordshire-based Mackintosh, who spent 12 years in the police force before leaving in 2011 to become a full-time writer, said she had been an unpublished author when she first came to the festival in Harrogate, North Yorkshire.
"I would like to thank my publishers and agent for supporting me, everybody who has read and recommended I Let You Go, and the crime writing community for their endless encouragement," she said on Thursday.
McDermid, a co-founder of the festival who won its best novel award in 2006, said it was "unlike any other in its warmth and generosity".
The 61-year-old Scot said the outstanding contribution award meant "a huge amount".
"This year sees the publication of my 30th novel and I can't think of a better way to celebrate that," she went on.
Rowling congratulated her "friend and colleague" McDermid on her "justly deserved" award and said she had "been showing us all the way for a long time now".
She added that the author's "favourable review" of her work as Galbraith had provided "one of Robert's proudest moments".
"She received a thank you note in fake handwriting, only to receive one two weeks later in my real handwriting when I was unwillingly unmasked."
Mark Billingham, another crime novel of the year nominee, called McDermid "the Queen of Crime", adding: "Long may she reign over us".
McDermid, he went on, had "represented this genre quite brilliantly all over the world, both in person and through her novels, which have earned her legions of fans and a place among the very greatest crime writers of all time."
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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.
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A former police officer's debut novel has won the Â£3,000 main prize at one of the UK's top crime-writing festivals.