The enantioselective hydrolysis of different (RS)-1,2-O-isopropylidene glycerol esters has been achieved with whole cells of Bacillus coagulans NCIMB 9365 furnishing the (S)-alcohol as the major enantiomer. The reaction is catalysed by a thermostable cell-bound carboxylesterase and improvement of the enantioselectivity has been achieved by heat treatment of the whole cells, which causes the knock-outs a non-enantioselective competing enzyme. Thermally-treated cells hydrolysed (RS)-1,2-O-isopropylidene glycerol esters with high enantioselectivity, the highest enantiomeric ratio (80–100) being observed for the benzoate. The biocatalyst displayed good stability and could be re-used after filtration for 12 cycles before showing significant loss of activity; repeated biotransformation batches allowed the recovery of 9.55 g/L of enantiomerically pure (S)-isopropylideneglycerol benzoate starting from 24.0 g/L of the racemic mixture.