The efficient chemoenzymatic synthesis of enantiopure 1,3-difunctionalized indane derivatives has been achieved. The corresponding cis and trans N-protected amino alcohols were successfully resolved by acetylation using lipase B, which is a biocatalyst isolated from Candida antarctica. All the possible isomers were obtained in very good chemical yields and ee values (>99 %). The utility of these compounds was subsequently shown by the preparation of orthogonally protected cis- and trans-indane-1,3-diamine using a Mitsunobu reaction. Both enantiomers of the trans isomer and a desymmetrized cis diastereomer were prepared in enantiopure form. Complete inversion of configuration during the Mitsunobu reaction was demonstrated by a combination of NMR techniques and molecular modeling. The utility and versatility of the strategy was also demonstrated by the selective deprotection of each nitrogen atom under mild reaction conditions.