The transport of free ions through highly under-expanded jet flows of neutral gases and in the presence of applied electric fields is investigated by continuum-based numerical simulations. In particular, numerical results are described that are relevant to ion flows occurring in the interface region of mass spectrometer systems. A five-moment mathematical model and parallel multi-block numerical solution procedure are developed for predicting the ion transport. The model incorporates the effects of ion-neutral collision processes and is used in conjunction with a Navier-Stokes model and flow solver for the neutral gas to examine the key features of the ion motion. The influences of the neutral gas flow, electric field, and flow field geometry on ion mobility are all carefully assessed. Several ions of varying mass and charge are considered, and the relative importance of competing effects (i.e. electric field and ion-neutral collision effects) is discussed. The capability of controlling the charged particle motions through a combination of directed neutral flow and applied electric field is demonstrated for high-speed, hypersonic jet flows.