We report a very facile microfluidic strategy for the fabrication of monodispersed fluorescent quantum dot (QD) embedded alginate barcodes. In this work, nano-sized calcium carbonate (CaCO₃) is added to the dispersed phase and used as the crosslinking agent for internal gelation of alginate. The as-prepared microspheres exhibit a uniform size distribution (CV = 2.7%). By tuning the quantity of the quantum dots with different emission wavelengths added to the dispersed phase, single color and multiple color barcode particles are successfully prepared in a flow focusing microfluidic device, which may be useful for various applications.