Wycombe District Council (WDC) met to decide on the Wycombe Air Park proposal in Booker on Monday night before voting against it.
Club owner Steve Hayes was hoping to move Wanderers and rugby union side Wasps from their Adams Park home to a new sports village which would include housing and community facilities.
The proposals, designed by Hayes' Wycombe Sports Development Ltd (WSDL) company, had been met with protest from supporter groups and environmental campaigners.
Wycombe Wanderers Trust said there were too many risks around the new stadium plans but hoped WSDL and Hayes come back to the negotiating table with a better offer.
"The cabinet's unanimous decision was taken on a combination of concerns in respect of development on an area of Green Belt and Area of Outstanding Natural Beauty and on financial prudence, given the uncertain benefits compared with the very real costs and risks associated with the proposal," it said.
"The Trust will be arranging discussions with Steve Hayes, and will welcome further discussions with WDC to discuss how Wycombe Wanderers can move forward at Adams Park, and the part that it can play in the next era of the club."