Amy, directed by Asif Kapadia, was named best documentary at the European Film Awards.
The film was condemned by her father Mitch Winehouse for painting the singer's family in a negative light.
Best European film went to Youth while British actress Charlotte Rampling was given a lifetime achievement.
Rampling also won best actress for her role in the British drama 45 Years at the event in Berlin on Saturday night.
Veteran actor Michael Caine received two trophies - he was presented with an honorary award and was also named best actor for Youth.
He said: "It's been 50 years and I've never won an award in Europe. And now I've won two in one evening. It's so strange because I (usually) sit in these audiences and just clap someone else."
The film, which co-starred American actors Paul Dano and Harvey Keitel, earned Italian filmmaker Paolo Sorrentino the award for best director.
Greek director and writer Yorgos Lanthimos picked up the screenwwriting award for his surreal drama The Lobster, which starred Irish actor Colin Farrell and Rachel Weisz.
The Irish film Song of the Sea was given the animation award.
German-Austrian star Christoph Waltz, currently on screens in the latest Bond adventure Spectre was presented with the award for European achievement in world cinema.
The European Film Academy was founded in 1988 and aims to promote films from across the continent.
A controversial documentary about the life and death of British singer Amy Winehouse has been honoured by the European Film Academy.