The interpretation of dark matter direct detection experiments is complicated by the fact that neither the astrophysical distribution of dark matter nor the properties of its particle physics interactions with nuclei are known in detail. To address both of these issues in a very general way we develop a new framework that combines the full formalism of non-relativistic effective interactions with state-of-the-art halo-independent methods. This approach makes it possible to analyse direct detection experiments for arbitrary dark matter interactions and quantify the goodness-of-fit independent of astrophysical uncertainties. We employ this method in order to demonstrate that the degeneracy between astrophysical uncertainties and particle physics unknowns is not complete. Certain models can be distinguished in a halo-independent way using a single ton-scale experiment based on liquid xenon, while other models are indistinguishable with a single experiment but can be separated using combined information from several target elements.