The reactions of coenzyme PQQ (pyrroloquinolinequinone) and several amino acids have been investigated in vitro. PQQ catalyses the oxidative decarboxylation of α-amino acids to afford the corresponding aldehydes under aerobic conditions. During the catalytic cycles, PQQ is gradually converted into oxazolopyrroloquinoline (OPQ) derivatives to be deactivated. Product analyses indicate that the reaction proceeds via an ionic mechanism that involves a carbinolamine-type adduct as a key intermediate. From this intermediate, direct decarboxylation (major path) and dehydration followed by decarboxylation and hydrolysis or by intramolecular cyclization (minor paths) competitively occur to give the quinol, the aminophenol and the OPQ derivative, respectively. In the reactions with β-hydroxy amino acids, tyrosine and tryptophan, oxidative dealdolation (Cα–Cβ fission) proceeds effectively. The similar ionic mechanism that involves the carbinolamine-type intermediate is suggested by the product analyses under both aerobic and anaerobic conditions.