The Onsager framework for linear irreversible thermodynamics provides a thermodynamically consistent model of mass transport in a phase consisting of multiple species, via the Stefan–Maxwell equations, but a complete description of the overall transport problem necessitates also solving the momentum equations for the flow velocity of the medium. We derive a novel nonlinear variational formulation of this coupling, called the (Navier–)Stokes–Onsager–Stefan–Maxwell system, which governs molecular diffusion and convection within a non-ideal, single-phase fluid composed of multiple species, in the regime of low Reynolds number in the steady state. We propose an appropriate Picard linearisation posed in a novel Sobolev space relating to the diffusional driving forces, and prove convergence of a structure-preserving finite element discretisation. This represents some of the first rigorous numerics for the coupling of multicomponent molecular diffusion with compressible convective flow. The broad applicability of our theory is illustrated with simulations of the centrifugal separation of noble gases and the microfluidic mixing of hydrocarbons.