Chiral myo‐inositol derivatives play key roles in cell‐signaling processes. Despite the relevance of these compounds, few syntheses of them rely on enantioselective catalytic reactions. Even fewer reports describe the use of desymmetrization of myo‐inositol derivatives. In fact, most routes involve resolution by derivatization. Thus, a symmetrical partially protected myo‐inositol derivative, 1,3‐di‐O‐benzyl‐myo‐inositol (1), was used as a substrate in fast lipase‐catalyzed desymmetrization reactions. Among the lipases tested, both Lipozyme RM‐IM and Lipozyme TL‐IM were effective in catalyzing the formation of the chiral acetate l‐(+)‐6‐O‐acetyl‐1,3‐di‐O‐benzyl‐myo‐inositol l‐(+)‐2 with high conversion (98–99 %) and ee (>99 %). Conversely, Novozyme 435 and Lipomod 34P as biocatalysts showed different regioselectivity, leading to the formation of the symmetrical 5‐O‐acetylated product. We were able to reuse TL‐IM lipase seven times without any noticeable decrease in the conversion. Acetate l‐(+)‐2 is a potential precursor of biologically active myo‐inositol derivatives and other relevant materials for cell biology studies. Depending on the choice of lipase, 1,3‐di‐O‐benzyl‐myo‐inositol (1) either undergoes desymmetrization to form l‐(+)‐6‐O‐acetyl‐1,3‐di‐O‐benzyl‐myo‐inositol (with Lipozyme RM‐IM or Lipozyme TL‐IM), or is transformed into the meso 5‐O‐acetyl derivative 3 (with Novozym 435).