Munich mayor Christian Ude said the 2022 bid "had failed" after all four regions, including the Alpine community of Garmisch-Partenkirchen and Munich voted against it after Munich had unsuccessfully pitched for the 2018 Games.
"I think it was not a problem with a concept but rather a growing criticism of parts of the population with mega sports events," Ude said.
Munich bid hopefuls needed to win all four elections in the communities where the Games would have been held but instead lost all four of them, some heavily.
Results in Garmisch showed 54 percent of the voters against the Games because of environmental, construction and financial concerns.
Munich residents voted 52 percent against the bid while citizens in Traunstein were even less enthusiastic about it with close to 60 percent against.
"We have to accept this result. Unfortunately, this is from our view a missed opportunity," German Olympic Sports Confederation General Director Michael Vesper said.
A total of 1.3 million were eligible to vote at the elections in Munich, Garmisch and the communities of Berchtesgadener Land and Traunstein.
Munich had attempted to become the first city to host the Summer and Winter Olympics, after staging the 1972 Summer Games.
"Environmental conscience and love of the home country of the citizens defeat commercialism and gigantism," said Hubert Weiger, chair of the Bavarian Nature Association, whose group was a staunch opponent of another bid.
Kazakhstan's Almaty and Ukraine's Lviv have announced their candidacies and China's state media reported that Beijing and the northern city of Zhangjiakou will jointly bid for the 2022 Games.
The deadline for bids with the International Olympic Committee is Nov. 14. Sochi will host next year's Winter Games while South Korea's Pyeongchang beat Munich for the 2018 Olympics.