This work focuses on fabrication of polyimide aerogel microparticles of diameter 200-1000 µm from a surfactant-free, two-phase, silicone oil/dimethylformamide (DMF) oil-in-oil (O/O) system using a simple microfluidic device. The polyimide sol prepared in DMF is turned into droplets suspended in silicone oil in the microfluidic device. The droplets are guided to a heated silicone oil bath to accelerate sol-gel transition and imidization reactions, thereby yielding spherical, discrete gel microparticles that do not undergo coalescence. The discrete gel microparticles are isolated and supercritically dried to obtain aerogel microparticles. The microparticle size distribution shows dependence on dispersed and continuous phase flowrates in the microfluidic channels. The microparticle surface morphology shows dependence on silicone oil bath temperature. The results are discussed in light of existing literature work on fabrication of solid microparticles, mesoporous microparticles, leading finally to a novel microfluidic process for continuous manufacturing of core-shell microparticles with mesoporous shell materials. Such particles find applications in absorption of noxious liquids and as hosts for catalysts.