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This paper reports the encapsulation of microparticles (mu-particles) and biomolecules using the layer-by-layer (LbL) nanoassembly technique with droplet microfluidic devices. This so-called droplet-LbL microchip consists of two microfluidic droplet generators, a microfluidic droplet-merging channel and a microfluidic mixing channel. The assembly of positive-charged PDDA layer on 3T3 cells has been successfully demonstrated, resulting in their surface potential change from -25.81 mV to 40.16 mV. The successful encapsulation of negative-charged mu-particles (polymethacrylate) within FITC-labeled protamine sulphate layer is also confirmed by their fluorescence image.