High-performance liquid chromatography with diode array (HPLC-DAD) and liquid chromatograph triple quadrupole mass spectrometry (HPLC-MS/MS) were used to characterize raw and fermented coffee pulps in terms of their phenolic composition and caffeine content. The qualitative analysis showed no significant differences between the raw and the fermented pulps. Free hydroxycinnamic acids (HAs) were mainly chlorogenic acids, with 5-caffeoylquinic acid as the major compound. Bound HAs released caffeic acids during alkaline hydrolysis, and no bound ferulic and p-coumaric acids were detected. The fermentation process allowed the detoxification of the pulp from caffeine by 50%, while significantly reducing the amounts of residue by 64%. Moreover, the fermented products could be further processed to provide high added-value molecules with potential industrial applications, providing a new source of income for the small coffee producers.