Herein, we report the utilization of a submicron Pickering emulsion (SPE) for the encapsulation of enzymes (e.g., lipase from Candida sp.) in water droplets that were solely stabilized by hydrophobic solid or mesoporous silica nanoparticles in toluene for use in biphasic reactions. The catalytic performance of encapsulated lipase was evaluated in the esterification of 1-hexanol and hexanoic acid under stirring-free conditions, which was favorable for maintaining enzymatic activity. Remarkably, the SPE significantly increased the specific activity of encapsulated lipase, owing to the exceptionally high water/oil interfacial area and short diffusion distance of the reagents in the SPE. With mesoporous silica nanoparticles, the activity of lipase was approximately 25.5- and 2.8-times higher than that of free lipase and encapsulated lipase in the micron Pickering emulsion, respectively. The higher water/toluene interfacial area was attributed to the smaller submicron-scale water droplets and the increase in the mass transfer of enzymes or substrates was further improved by using mesoporous Pickering stabilizers. In addition, the encapsulated lipase in SPE also demonstrated excellent stability and could be recycled up to 15 times without significant loss of activity.