Bayern Munich have around 12 million fans in Germany, a number that is dwarfed only by those who dislike the club with equal passion. And Bayern would not have it any other way. They actively play on a heightened sense of Bavarian-ness, on a confidence that verges on arrogance and describe themselves as "a family" to create an "us and them" dynamic. "We cultivate this polarisation," Karl-Heinz Rummenigge, the CEO, says. "Partly because it means that we have constant media exposure."

This aggressive marketing – and continued success on the pitch, with the Champions League final against Chelsea on Saturday – has made Bayern a blue-chip brand, representing West Germany's golden, Franz Beckenbauer-led era of the 70s and the promise of the current generation. But there is also a very different side to "FC Hollywood", a part of the Bayern story that is still unknown to most supporters and that has also only been recently embraced by the club after nearly 80 years of awkward silence.

Bayern were founded in the bohemian quarter of Schwabing, and were very much a Jewish club before the second world war, with a Jewish president and a Jewish manager. As a consequence, Bayern were targeted by the Nazis but players and officials continued to defy the regime with small acts of personal courage. "All those things were forgotten in the post-war years," said Dietrich Schulze-Marmeling, the author of 2011's award-winning Der FC Bayern und seine Juden (FC Bayern and their Jews). "Bayern's success in the 60s and 70s submerged the past, and West German society on the whole only started to look back at the Holocaust in earnest in 1979, in any case."

On the club's founding charter from 1900, two out of 17 signatories were Jewish. One of them, the Dortmund-born artist Benno Elkan, would later emigrate to London and become a prominent sculptor: on commission from Westminster, he built the seven-branched Candelabra (Menorah) that stands outside the Israeli parliament in Jerusalem. From 1911, Bayern were led by Kurt Landauer, the son of a wealthy Jewish businessman, and the team were coached by a succession of Jewish coaches, including the Austro‑Hungarian Richard "Little" Dombi, who went on to manage Barcelona and Feyenoord. Landauer's commitment and Dombi's knowhow secured a first German championship for Bayern in 1932. Landauer had to resign, along with a number of other Jewish members and officials, when Hitler seized power a few months later and fled to Switzerland after 33 days in the Dachau concentration camp.

Bayern were discredited as a Judenklub by the Nazis but resisted its cooptation. In 1934, Bayern players were involved in a brawl with Nazi brownshirts. Two years later, the Bayern winger Willy Simetsreiter made a point of having his picture taken with Jesse Owens, who enraged Hitler by winning four gold medals at the Berlin Olympics. The full-back Sigmund Haringer narrowly escaped prison for calling a Nazi flag parade a "kids' theatre", and the captain, Conny Heidkamp, and his wife hid Bayern's silverware when other clubs heeded an appeal from Reichsmarschall Herman Göring to donate metal for the war effort. The most symbolic act of defiance occurred in Zurich in 1943. After a friendly against the Swiss national team, the Bayern players lined up to wave at the exiled Landauer in the stands.

Landauer returned to Munich after the war and once again became Bayern president until 1951. But his legacy became lost. Club publications simply mentioned that he had to leave Germany "on political-racial grounds". "The word 'Jew' was assiduously avoided," said Schulze-Marmeling. At the turn of the century, a wave of academic books and newspaper articles renewed interest in the Landauer era but the Bayern leadership were unsure as to how they should react. Bayern's general manager, Uli Hoeness, fobbed off an inquisitive reporter by saying he "wasn't alive at the time", and vice-president Fritz Scherer later admitted that the club did not want to emphasize its Jewish roots for fear of "negative reactions". "We don't want to provoke something," Scherer said. Schulze-Marmeling suspects that commercial interests in Asia may also have been the reason why Bayern sought to play down their Jewish heritage.

The club's attitude has changed markedly in recent years, however. The club's Ultras have celebrated Landauer and Rummenigge has acknowledged him as "the father of the modern FC Bayern". The club also donated part of the money that enabled the Jewish amateur club TSV Maccabi Munich to build a pitch bearing Landauer's name in 2010. The ground was inaugurated with a friendly against Bayern's "All-Star-Team".

The Landauer years will take pride of place in the Erlebniswelt museum the club are opening in the Allianz Arena this summer. "I've been in the club for many years but had little idea about all these amazing stories," said Hans-Peter Renner, the museum's content director. "It's been profoundly moving to learn about all these people and the things they did for the club."