Subtilisin Carlsberg (SC) was immobilized and stabilized on magnetically-separable mesoporous silica (Mag-MSU-F) in the form of nanoscale enzyme reactors (NERs) based on the ship-in-a-bottle mechanism. Stabilized NERs of SC (NER-SC) were freeze-dried and successfully used for the transesterification of N-acetyl-L-phenylalanine ethyl ester with n-propanol in isooctane. Magnetic separation of Mag-MSU-F facilitated the repeated usages of stable NER-SC. This is the first demonstration for the use of stable and magnetically-separable NERs in an organic solvent, which has the potential for environmentally-friendly synthesis using enzymes in organic solvents.