We have derived a novel reverse microemulsion process to impose temporal and spatial control of self-assembly. The ability of this process to transform morphology and size has been demonstrated using an enzyme-responsive dipeptide, Fmoc-Phe-Tyr-phosphate. In the presence of phosphatase, these molecules self-assemble into nanofibers of about 28nm in aqueous solution. By controlling the self-assembly process with an enzymatic trigger and confining it within nanoscale reverse micelles, the same molecules are fabricated into nanoparticles of around 6.5nm. We further investigate the morphology and size control of peptide assemblies by changing the process parameters, including the ratio of various reagents and incubation time. The resulting nanostructures are characterized by transmission electron microscopy and dynamic light scattering. The possible process for peptide nanoparticle formation inside reverse micelle is proposed according to the results. This method is applicable to other stimuli-responsive self-assembling blocks.