The discovery or development of thermoalkalophilic lipases that show high levels of catalytic activity in organic solvents would have important industrial ramifications. However, this goal is yet to be achieved because organic solvents induce structural changes in lipases that suppress their catalytic abilities. A deep understanding of these structural changes to lipases in the presence of organic solvents is required before strategies can be devised to stop them from occurring. In this work, we investigated the effects of an organic reaction medium, toluene, on the structure of the Bacillus thermocatenulatus lipase BTL2 using MD simulation. The main aims were to identify the regions of the protein that are particularly sensitive to the presence of an organic solvent, and how the presence of a hydrophobic medium affects the overall stability of the enzyme. Upon analyzing how the behavior of the enzyme differed in aqueous and hydrophobic media, it was found that many significant zones of the protein suffer in the presence of an organic solvent, which increases the rigidity of the system. This was readily apparent when we investigated important noncovalent interactions (salt bridges) and probed how distances between the atoms of the catalytic triad Ser114, Asp318, and His359 change in the presence of toluene. Moreover, the high tendency for the system to destabilize in toluene was explained by the results of FoldX calculations. Calculations showed that the addition of a small amount of water to the hydrophobic reaction environment should restore the required flexibility of BTL2. The insights gained from the analysis of our simulations allowed us to propose a modification of BTL2, the G116P mutation, that should result in the structural behavior of BTL2 in organic solvent being closer to that of BTL2 in water.