We have identified the existence of different modes of binding the enantiomers of 2-methyl-branched carboxylic acids to a lipase active site by rational substrate engineering. Similar to hydrolysis, previously investigated, we have now evidence for differential binding modes in the Candida rugosa lipase-catalyzed esterifications in cyclohexane. The relevance of considering two different binding modes to understand lipase enantiorecognition is demonstrated by introducing bulky substituents on a chiral carboxylic acid which impose a different orientation of the substrate acyl chain in the active site of Candida rugosa lipase. With this substrate engineering approach based on molecular modeling it is thus possible to markedly alter the enantioselectivity of the lipase. Examples from hydrolysis and new results from esterifications in an organic solvent are presented and discussed.