Despite the key role of flavan-3-ols in many foods, very little is yet known concerning the modification of their chemical structures through food processes. Degradation of model media containing (-)-epicatechin and procyanidin B2, either separately or together, was monitored by RP-HPLC-DAD-ESI(-)-MS/MS. Medium composition (aqueous or lipidic) and temperature (60 and 90 °C) were studied. In aqueous medium at 60 °C, (-)-epicatechin was mainly epimerized to (-)-catechin, but it was also oxidized to "chemical" dimers, a "chemical" trimer, and dehydrodi(epi)catechin A. Unlike oxidation, epimerization was enhanced at 90 °C. In lipidic medium, epimerization proved slow but degradation was faster. Procyanidin B2 likewise proved able to epimerize, especially at 90 °C and in aqueous medium. At high temperature only, the interflavan linkage was cleaved, yielding the same compounds as those found in the monomer-containing model medium. Oxidation to procyanidin A2 was also evidenced. With little epimerization and slow oxidation even at 90 °C, procyanidin B2 proved more stable in lipidic medium. Synergy was also observed: in the presence of the monomer, the dimer degradation rate increased 2-fold at 60 °C. This work states for the first time the presence of newly formed flavan-3-ol oligomers in processed cocoa.