Features Cacao, a student at Micro-Grand Academy studying magic. One day, while his magic class teacher, Ghana, is performing a spell to summon a tree spirit, Cacao finds and eats some chocolate, which turns out to be 200 year old magical chocolate. After eating the chocolate he becomes drunk and causes a wreck. During this, he interferes with Ghana's spell, letting the spirit, Hinano, escape. She inhabits the body of a marionette, who then moves in with Cacao.

Subsequent episodes of Trouble Chocolate have little connected storyline. Rather, the show is a parody of other anime.

The dubbed dialogue in Trouble Chocolate often bears little or no resemblance to the original script, as opposed to the normal convention of translating the words as directly as the change in lip-sync will allow.