Flavan-3-ols are claimed to be responsible for the cardioprotective effects of cocoa. Alkalized cocoa powder (ALC), commonly used for many non-confectionary products, including beverages, provides less (+)-catechin, (−)-epicatechin, and procyanidins and more (−)-catechin than nonalkalized cocoa powder (NALC). This may affect the plasma appearance of monomeric flavan-3-ol stereoisomers after consumption of NALC vs. ALC. Within a randomized, crossover trial, 12 healthy nonsmokers ingested a milk-based cocoa beverage providing either NALC or ALC. Blood was collected before and within 6 h postconsumption. (+)-Catechin, (−)-catechin, and epicatechin were analyzed in plasma by HPLC as sum of free and glucuronidated metabolites. Pharmacokinetic parameters were obtained by a one-compartment model with nonlinear regression methods. For epicatechin in plasma, total area under the curve within 6 h postconsumption (AUC0–6h) and incremental AUC0–6h were additionally calculated by using the linear trapezoidal method. After consumption of NALC and ALC, (+)-catechin and (−)-catechin were mostly not detectable in plasma, in contrast to epicatechin. For epicatechin, total AUC0–6h was different between both treatments, but not incremental AUC0–6h. Most kinetic parameters were similar for both treatments, but they varied strongly between individuals. Thus, epicatechin is the main monomeric flavan-3-ol in plasma after cocoa consumption. Whether NALC should be preferred against ALC due to its higher (−)-epicatechin content remains unclear with regard to the results on incremental AUC0–6h. Future studies should investigate epicatechin metabolites in plasma for a period up to 24 h in a larger sample size, taking into account genetic polymorphisms in epicatechin metabolism and should consider all metabolites to understand inter-individual differences after cocoa intake.