Color is one of the most important visual attributes of food and is directly related to the perception of food quality. The interest in natural colorants, especially β-carotene that not only imparts color but also has well-documented health benefits, has triggered the research and development of different protocols designed to entrap these hydrophobic natural molecules to improve their stability against oxidation. Here, we report a versatile microfluidic approach that utilizes single emulsion droplets as templates to prepare microparticles loaded with natual colorants. The solution of β-carotene and shellac in the solvent is emulsified by microfluidics into droplets. Upon solvent diffusion, β-carotene and shellac co-precipitates, forming solid microparticles of β-carotene dispersed in the shellac polymer matrix. We substantially improve the stability of β-carotene that is protected from oxidation by the polymer matrix and achieve different color appearances by loading particles with different β-carotene concentrations. These particles demonstrate great promise for practical use in natural food coloring.