The acyltransferase from Mycobacterium smegmatis (MsAcT) complements the well-established acylation activity of hydrolases in organic solvents with its activity to perform acylation reactions (among other reactions) in an aqueous environment. The enzyme’s potential is however limited, due to its poor regio- and stereoselectivity with enantioselectivities (E-values) below 20 for bulky (aromatic) substrates. By applying computer-guided rational design, a library of single variants was designed that allowed conversion of a set of previously challenging substrates with good activity and E-values up to >200. The computational predictions were found to be in agreement with experimental data, which in turn allowed for the generation of even more active and selective double variants. Overall, the produced set of variants provides a toolbox for the enantioselective acylation of challenging alcohols in water, effectively contributing to an alternative to reactions in organic solvents.