The bioimprinting effect in sol‐gel immobilization of lipases was studied to develop efficient novel immobilized biocatalysts with significantly improved properties for biotransformations in continuous‐flow systems. The bioimprinting candidates were selected systematically among the substrate mimics already found in the active site of experimental lipase structures. Four lipases (Lipase AK, Lipase PS, CaLB and CrL) were immobilized by a sol‐gel process with nine bioimprinting candidates using various combinations of tetraethoxysilane (TEOS), phenyltriethoxysilane (PhTEOS), octyltriethoxysilane (OcTEOS) and dimethyldiethylsilane (DMDEOS) as silica precursors. The biocatalytic properties of the immobilized lipases were characterized by enantiomer selective acylation of various racemic secondary alcohols in two different multisubstrate systems (mixture A: a series of alkan‐2‐ols rac‐1a–e and mixture B: heptan‐2‐ol rac‐1f and 1‐phenylethanol rac‐1g). Except with Lipase AK, the most significant activity enhancement was found with the imprinting molecules already found as substrate mimics in X‐ray structures of various lipases. The synthetic usefulness of the best biocatalysts was demonstrated by the kinetic resolution of racemic 1‐(thiophen‐2‐yl)ethanol (rac‐1h) in batch and continuous‐flow systems.