Proximity effects in layered heterostructures are commonly represented by static parameters fitted to first-principles band structures, an approximation that usually discards the energy dependence of interlayer hybridization, momentum transfer, and spatial structure. We address this limitation by deriving a dynamical proximity operator directly from density functional theory by downfolding the heterostructure Kohn-Sham Hamiltonian onto a fixed low-energy target Wannier subspace. We demonstrate the method for three different graphene heterostructures coupled to magnetic and semiconducting substrates. Graphene/hBN/Co(0001) exhibits proximity-induced exchange resonances driven by hybridization with Co states. Graphene/PtSe₂ develops a sublattice-selective, intervalley-coherent, proximity-induced coupling. For graphene/WSe₂, we identify the spatial modulation of both Rashba and valley-Zeeman proximity-induced spin-orbit couplings. The method determines the full microscopic structure of the proximity coupling from first principles, providing input for transport and correlated-phase calculations.