The organization's executive director Laura Lansink has penned an open letter to the public expressing its concerns, saying Singh has given food unfit for human consumption to some of the food banks.
The letter also said he had taken advantage of volunteer labour to grow produce that was then sold for profit instead of being donated directly to charities.
"It's absolutely imperative to us that donors and volunteers know where their time and their money is going," Lansink said. "We felt we had to wade into this whole situation."
The concerns started in 2013 when the Surrey Food Bank, which was at one point Singh's biggest recipient, quietly cut off its ties over concerns of the quality of his produce.
"If there is a need to go through perishable items that are rotting or of inferior quality, that takes a tremendous amount of time from our volunteers," said Marilyn Herrmann, executive director of the Surrey Food Bank.
"I am delighted when we're offered support. With God's Little Acre, it just didn't work out."
Food Banks B.C., which manages the province's food banks, said only one of their 96 members has received any produce from Singh since 2013.
The Greater Vancouver Food Bank is the exception — Singh donated approximately 1,400 kilograms of mixed produce in 2014 and was also paid for 15,000 kilograms of carrots and potatoes. He also made a donation of approximately 23,000 kilograms of produce to them in 2013.
'Mickey Mouse' operation
Since the food banks have refused to do business with him, Singh said he has instead given his produce to local soup kitchens and schools, as well as the needy who come to his farm.
When reached by CBC News, Singh maintains his intentions have always been good, but he could have been more forthcoming with his supporters. Singh said he runs a "Mickey Mouse" operation with no clear record of where his food has been going.
"I am now actively changing the structure and accountability to make it professional and accountable," he said in an email, adding that he plans to keep a full list of soup kitchens and schools that receive his produce.
He runs what he calls "B.C.'s Poorest Farm," relying mostly on some 1,100 volunteers to keep costs down. He has almost reached his crowdfunding goal of $50,000 to buy used tractors and equipment, among other things, and said he has donated roughly 190,000 kilograms of produce in the last four years to food banks.
Singh admitted he hasn't been fully honest that the food banks have cut off ties with him, but he also said he has been misunderstood.
"I kept this secret from the general public because if the public were to find out that the Surrey Food Bank treated me this way after all I did, there would be a huge backlash," Singh posted on Facebook.
Many of his supporters and donors have also posted to his Facebook page, verifying that they have received donations from his farm and that the bottom line is that he does good deeds.
Still, Food Banks B.C. wants more accountability and transparency from Singh, before it puts its faith back in God's Little Acre.
"It's disturbing," said Lansink. "We wanted to step up because we felt there wasn't the kind of transparency that donors and volunteers should expect."