The transesterification of 3-[(β-cyclodextrinyl)succinamido]propane-1,2-diol with fatty esters catalyzed by immobilized lipase from Mucor miehei occurred with very different conversions of the two diastereoisomers [(R)- or (S)-amidopropanediol]. The highest conversion observed with the (S)-amidopropanediol can be related to either lipase diastereoselectivity or substrate specificity. To investigate the diastereoselectivity of the lipase, diastereoisomers of the methylated β-cyclodextrin were replaced by methylated glucopyranoside or methylleucine. No discrimation of the diastereoisomers by lipase was observed. Molecular modeling was performed to assess the lipase selectivity towards the two diastereoisomers. It was found that the (R)-amidopropanediol is stabilized by hydrogen bonding with the cyclodextrin rim resulting in less reactive hydroxy groups.