Colloidal crystals show structural colors through wavelength-selective diffraction at photonic stopbands. Here, we design photonic Janus microspheres with a controlled magnetic moment for programmable structural color switching. The Janus microspheres are produced from microfluidically produced paired drops of two distinct photocurable resins. The lighter resin contains magnetic nanoparticles and carbon black, whereas heavier one contains silica particles at a high-volume fraction. The paired drops spontaneously align vertically due to the density asymmetry. The magnetic moment is assigned in the vertically aligned drops by aligning magnetic nanoparticles with an external field and capturing them through photopolymerization. Silica particles in the heavier compartment spontaneously form crystalline arrays due to interparticle repulsion, developing structural colors. The resulting photonic Janus microspheres vertically align without an external field, like a roly-poly toy, so that carbon-black-laden compartments face upward. With an external magnetic field, the Janus microspheres align their magnetic moment to the field and display structural colors. Importantly, the direction of the magnetic moment is set by the direction of the external field during photopolymerization, which enables the simultaneous manipulation of orientations of distinct photonic Janus microspheres in a programmed manner. These photonic Janus microspheres are potentially useful as active color inks for anti-counterfeiting tags.