Selective deprotection of functional groups using different wavelengths of light is attractive for materials synthesis as well as for achieving independent photocontrol over substrates in biological systems. Here, we show that mixtures of recently developed visible light-absorbing BODIPY-derived photoremovable protecting groups (PRPGs) and a coumarin-derived PRPG can undergo wavelength-selective activation, giving independent optical control over a mixture of photocaged substrates using biologically benign long-wavelength light.