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 wakanga uri weGerman Super Cup neBorussia Dortmund, neBayern ichirasikirwa ne4 <unk> 2. Mukombe wake wekutanga neBayern yaive 2013 UEFA Super Cup
, vachikunda muvengi wavo wenguva refu José Mourinho, uyo akanga achangodzokera kunodzidzisa kuChelsea. Bayern yakakunda Chelsea ine varume gumi mukubudirana pfuti mushure mekunge Manuel Neuer aponesa Romelu Lukaku.