Bayern München II

The team's first appearance in the top-league of Bavarian football, the southern group of the Amateurliga Bayern, came in 1956, when it won the tier-four 2nd Amateurliga Oberbayern A and advanced to the next level through the promotion round. After finishing its first season in this league in mid-table, it ended 1957–58 as runners-up, two points behind local rival Wacker München. It repeated this achievement in 1960–61, this time coming second to 1860 Munich II. Both reserve sides then descended in the league table and, in 1963, when the German football league system was severely altered, they both missed the cut-off for the new single-tier Amateurliga Bayern. Bayern Amateure had to finish seventh to qualify but came only 14th and found itself grouped in the new tier-four Landesliga Bayern-Süd.

It took the team four seasons in this league to work its way back up, improving year by year and, in 1966–67, it finished first and earned promotion back to the Bayernliga. Bayern started well in the league, coming fourth in the first year, but then declined and was relegated again in 1971. It only took two seasons this time for the team to return to the third division and another league win in 1973 moved the team back up.

For the next 21 seasons, the team was to be a member of the Bayernliga without interruption. However, in all the 21 seasons there, the team could never win the league either, being ineligible for promotion from there to professional football anyway.

The team had few bad seasons in this time, coming relatively close to relegation only once, in 1982. It managed three runners-up finishes in the league, in 1983, 1984 and 1987 and generally existed as an upper-table side.

In 1994, with the introduction of the new tier-three Regionalliga Süd, the team qualified comfortably. It was to be a long-term member of this league, too, belonging to it until 2008, when the 3. Liga was formed. After mostly finishing in mid-table in the league, Bayern earned its first league title in over 30 years when it won the Regionalliga in 2004. Being already a member of the highest league in which reserve teams are permitted, the side could not take up promotion to the 2nd Bundesliga and had to stay at this level. In 2005, all reserve sides of clubs in the first and second Bundesliga changed their name from Amateure to II, meaning FC Bayern Munich Amateure became FC Bayern Munich II.

In 2008, the team earned promotion to the new 3. Liga, finishing eighth when a top-ten finish was needed. The club played at this level for three seasons before suffering relegation to the Regionalliga in 2010–11. It was the first time since 1973 that the team would not play in the third division and also meant the end of Hermann Gerland as the team's coach.

After coming second in the inaugural Regionalliga Bayern season in 2012–13, the team won the league the following year. This entitled the club to enter the promotion round to the 3. Liga. After two games against Regionalliga West champions Fortuna Köln, they lost due to the away goal rule, making their opponents one of the three promoted teams to the third division.

In 2019, Bayern Munich II earned promotion to the 3. Liga, after winning Regionalliga 2018–2019 and defeating Wolfsburg II in the two-game promotion-playoff (1–3 and 4–1). The following season, while placing 15th after the first half of the season, Bayern Munich II won the 3. Liga. However, since secondary teams aren't eligible for promotion to 2.Bundesliga, Bayern Munich II remained in 3. Liga for the 2020–21 season. Bayern II failed to defend their 3. Liga title in the 2020-21 season, finishing 18th, and were relegated to the Regionalliga Bayern.