There was no substantial armed resistance against Allied occupation. The German population — who were, by 1945, war-weary and traumatised by more than a decade of totalitarian rule — were generally compliant with the occupying forces.

In the final months of the war, Himmler and the SS did develop a plan for a 'stay-behind' guerrilla force called Werwolf to carry on the fight against the Allies. But there's a lot of mythology around Werwolf (which was certainly more successful as propaganda than actual resistance) and most serious scholars have long since concluded that its impact — if the plan was ever even put into motion — was minimal.

Anthony Beevor's conclusion in Berlin: The Downfall 1945 is pretty illustrative of the mainstream view of the Werwolf programme:

Ultimately, Werwolf achieved very little, apart from a couple of assassinations — the mayors of Aachen and Krankenhagen — and the intimidation of civilians. Hitler Youth chalked slogans on walls such as, ‘Traitor take care, the Werwolf is watching.’ Both [Otto Skorzeny, the noted German commando leader] and [the 'General Inspector for Special Defence' Hans-Adolf Prützmann] seem to have become less enamoured of the project as the allies closed in – if one is to believe Skorzeny’s account in his interrogation. (Prützmann committed suicide after one brief interview.) In any case, Himmler also had a change of heart in mid-April, just when negotiations via Sweden were on his mind. He instructed Prützmann to change Werwolf activity ‘to that — exclusively — of propaganda’. The only problem was that the Werwolfsender radio transmitter, under the control of Goebbels, continued to order partisan action.