Procyanidins are metabolised by endogenous gastrointestinal microflora into several small molecules that may exert systemic effects. However, the metabolic pathways of procyanidins are still largely uncharacterised. The aim of this study was to evaluate the colonic metabolism of procyanidins (catechin, epicatechin, epicatechin gallate, epigallocatechin gallate and dimer B2) and alkaloids (theobromine and caffeine) by an in vitro colonic fermentation model using rat colonic microflora. Simultaneously, a nuts-cocoa cream was incubated and the colonic metabolism of procyanidins and alkaloids was evaluated. Results showed that most of the procyanidins tested were catabolised after 24–48h of fermentation. Fermentation of the dimer B2 did not produce the same catabolic compounds as epicatechin fermentation and differences were observed between the fermentation of catechin and epicatechin. The alkaloids were not metabolised by the colonic microflora and this fact was verified in vivo. The results showed an intense metabolism of procyanidins and poor metabolism of alkaloids.