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The assembly of two different kinds of colloidal particle-based photonic structures into an individual micro-object can achieve multifunctionality. In this study, core–shell photonic microcapsules with dual structural colors and photonic stop bands were prepared through a standard microfluidic technique. Photocurable resin suspension of silica nanoparticles and an aqueous suspension of nanogels were used as shell and core parts of microcapsules, respectively. The structural colors of shells and cores can be tuned by adjusting the concentrations of silica nanoparticles and soft nanogels in their corresponding suspensions. The individual microcapsules possess two distinct stop bands when the two suspensions are combined appropriately. Remarkably, the color information of the core part cannot be directly viewed at a macroscopic level (such as visual inspection) but can be detected at a microscopic scale (such as optical microscopy observation). The color information hidden enables the capability for information encryption and has potentially critical applications in anti-counterfeiting, display, and other fields.