A large body of knowledge about magnetism is attained from models of interacting spins, which usually reside on magnetic ions. Proposals beyond the ionic picture are uncommon and seldom verified by direct observations in conjunction with microscopic theory. Here, using inelastic neutron scattering to study the itinerant near-ferromagnet MnSi, we find that the system’s fundamental magnetic units are interconnected, extended molecular orbitals consisting of three Mn atoms each rather than individual Mn atoms. This result is further corroborated by magnetic Wannier orbitals obtained by ab initio calculations. It contrasts the ionic picture with a concrete example and presents an unexplored regime of the spin waves where the wavelength is comparable to the spatial extent of the molecular orbitals. Our discovery brings important insights into not only the magnetism of MnSi but also a broad range of magnetic quantum materials where structural symmetry, electron itinerancy, and correlations act in concert.