I te 16 o Hanuere 2013, i panuitia ka riro a Guardiola hei kaiwhakahaere o te karapu Bundesliga Bayern Munich i muri i te waa 2012-13, hei whakakapi i a Jupp Heynckes mo te waa e whai ake nei. I korero ia i tana huihuinga panui tuatahi hei kaiwhakahaere Bayern, i te 24 o Pipiri 2013, i te reo Tiamana, ana i whai waahi ia ki tana whakangungu tuatahi i nga ra e rua i muri mai. Ko tana tukinga tuatahi ko te Super Cup Tiamana ki a Borussia Dortmund, ka ngaro a Bayern 4-2. Ko tana tohu tuatahi me Bayern ko te 2013 UEFA Super Cup
, i hinga i tana hoa whawhai o mua a José Mourinho, i hoki mai nei ki te whakangungu i Chelsea. I whiua e Bayern a Chelsea tekau-tangata i roto i te pupuhi i muri i te whakaora a Manuel Neuer i te whiu a Romelu Lukaku.