The thiamine diphosphate (ThDP)-dependent pyruvate decarboxylase from Acetobacter pasteurianus (ApPDC) catalyzes the carboligation of aldehydes that yields (R)-2-hydroxy ketones with high chemoselectivity in mixed carboligations of aliphatic donor and aromatic acceptor aldehydes. On the basis of the crystal structure of ApPDC, which was determined to a resolution of 2.75 Å, and biochemical data, we mapped the active site. This enabled us to design variants with tailor-made catalytic activities by modifications of the residues E469 and W388. Although the exchange of W388 by smaller amino acids yields variants with higher carboligase activity due to an increased access to the active site, the exchange of E469 to glycine opens the so-called S-pocket in ApPDC for aromatic aldehydes and thus alters the stereoselectivity. The variant ApPDC-E469G provides access to (S)-phenylacetylcarbinol derivatives by enzymatic carboligation with a good stereoselectivity of up to 89 % enantiomeric excess. The variant nicely complements the toolbox of ThDP-dependent enzymes, which now gives access to all stereo- and regioisomers of the asymmetric aliphatic–aromatic cross-benzoin-like condensation. We prove that optimal stabilization of both aldehydes in the active site is essential to gain high yields and high selectivities.