A comparative QM/MM study of the racemization reaction of two different substrates of mandelate racemase, propargylglycolate and mandelate, has been carried out. The results have been compared with those previously obtained for vinylglycolate using the same methodology. The crucial point in understanding the catalytic activity seems to be the stabilization of the anionic intermediates in the active site. Our results indicate that there are at least three different mechanisms for the racemization. It is in the third mechanism, the most favorable one, where the modulation of the rate of racemization of β,γ-unsaturated α-hydroxycarboxylates by mandelate racemase is in accord with the experimental observations. Thus mandelate is the substrate that undergoes racemization by the enzyme at the highest rate. This is due to the highest efficiency of mandelate to delocalize the extra negative charge of the transition state and the intermediate that are found along the reaction path of the α-proton abstraction. The role of propargylglycolate as an inactivator of mandelate racemase has also been studied in comparison to its activity as a substrate of the enzyme.