Multi-color photons are prominent candidates for carrying quantum information, as their unlimited dimensionality allows for novel qudit-based schemes. The generation and manipulation of such photons takes place in nonlinear optical media, and the coupling between the different frequency bins can be engineered to obtain the desired quantum state. Here, we propose the design of a frequency-domain Stern–Gerlach effect for photons, where quantum entanglement between the spatial and spectral degrees of freedom is manifested. In this scheme, orthogonal frequency-superposition states can be spatially separated, resulting in a direct projection of an input state onto the frequency-superposition basis. We analyze this phenomenon for two-color qubits and three-color qutrits, and present a generalized wavelength-domain analog of the Hong–Ou–Mandel interference with distinguishable photons. Our results pave the way toward realization of single-element, all-optically controlled spectral-to-spatial beam splitters and tritters that can benefit quantum information processing in the frequency domain.