 On 16 January 2013, zvakaziviswa kuti Guardiola aizotora pamusoro sezvo maneja Bundesliga kirabhu Bayern Munich pashure 2012-13 mwaka, achitsiva Jupp Heynckes nokuda rakatevera mwaka. Akataura musangano wake wekutanga wevatori venhau semurairidzi weBayern, musi wa24 Chikumi 2013, muchiGerman, uye akaita musangano wake wekutanga wekudzidzira mazuva maviri gare gare. Mutambo wake wokutanga wepamutemo wakanga uri weGerman Super Cupvachirwa neBorussia Dortmund, neBayern ichirasikirwa 4-2. Mukombe wake wekutanga neBayern yaive 2013 UEFA Super Cup, achikunda muvengi wenguva refu José Mourinho, uyo anga achangodzokera kunodzidzisa kuChelsea. Bayern yakakunda Chelsea ine varume gumi mukubudirana pfuti mushure mekunge Manuel Neuer aponesa Romelu Lukaku. 