Heeley Farm in Sheffield secured the majority of local votes and won a £50,000 grant. The money will pay for a new "animals in therapy" centre, which will be used by children and people with learning difficulties.
But John le Corney, who works at the farm, said: "We are a well-established organisation that has been around for 25 years and have 40-50 staff, so we found it easy to fill in the application. I think that's the problem with the People's Millions - it doesn't operate on a level playing field. It's unfair if you are a small organisation that relies totally on volunteers and is not used to filling in application forms like we are. However, I do think it helped bring the local community together."
Le Corney added: "When I first heard about it I thought 'God, not another competition; I bloody hate competitions'. But we need funding, so we have to pursue every option."
Heeley Farm spent £500 of its own money to gather support before its pitch on regional television.
The Big Lottery Fund has commissioned extensive research to assess the views and experiences of all winners and losers throughout the People's Millions process, which is expected to be completed by the end of the month. An early analysis of the results shows that 17 of the winners had received lottery funding before, whereas 30 had not.
Another winner, Claire Peeters from Ecoworks in Nottingham, said she believed that the process favoured telegenic projects. Ecoworks offers therapeutic horticulture for people with mental health problems.
"I think certain projects won't win because they don't capture the public's imagination," she said. "We were up against a beekeeping project, which I liked, but it was too niche and didn't tug at the heartstrings."
She added: "It's been a huge emotional investment in a way that applying for a normal grant would never be."
A spokesman for the Big Lottery Fund disagreed that there was unfairness in the process. He said: "The results have shown that the public has chosen to back the projects closest to their hearts, regardless of the type of organisation running them."