The National League North club wore a special one-off rainbow shirt for their game against Bradford (Park Avenue) last season.
The initiative gained plaudits worldwide and the colourful strip now sits in the National Football Museum.
"We believe it will be the first time anywhere in the world that a senior football club has worn a kit solely modelled on the LGBT Pride Flag," Alty director Bill Waterson said back in February.
"Altrincham will, therefore, be creating a small moment of football history."
After taking home the award at last night's grass-roots heroes awards, Altrincham tweeted their gratitude.
"Thank you, @Cheshire_FA!" the club wrote on their official Twitter account.
"Football is a sport to be played and enjoyed by everyone on the planet, we just pushed that conversation along."