Rubuta ci gaba don wannan sakin layi - A ranar 16 ga Janairu, 2013, an ba da sanarwar cewa Guardiola zai zama kocin kulob din Bundesliga Bayern Munich bayan kakar 2012-13, ya maye gurbin Jupp Heynckes a kakar wasa mai zuwa. Ya yi jawabi ga taron manema labarai na farko a matsayin kocin Bayern, a ranar 24 ga Yuni, 2013, a Jamusanci, kuma ya yi zaman horo na farko kwana biyu bayan haka. Wasansa na farko na hukuma shi ne gasar cin kofin Jamus da Borussia Dortmund, inda Bayern ta yi rashin nasara 4-2. Kofinsa na farko tare da Bayern shine 2013 UEFA Super Cup
, ta doke abokin hamayyarta José Mourinho, wanda ya dawo ya horar da Chelsea. Bayern ta doke Chelsea da 'yan wasa goma bayan Manuel Neuer ya ceci Romelu Lukaku.