We identify the possible ground states for a mixture of two superfluid condensates (one neutral, the other electrically charged) using a phenomenological Ginzburg-Landau model. While this framework is applicable to any interacting condensed-matter mixture of a charged and a neutral component, we focus on nuclear matter in neutron star cores, where proton and neutron condensates are coupled via non-dissipative entrainment. We employ the Skyrme interaction to determine the neutron stars equilibrium composition, and hence obtain realistic coefficients for our Ginzburg-Landau model at each depth within the stars core. We then use the Ginzburg-Landau model to determine the ground state in the presence of a magnetic field. In this way, we obtain superconducting phase diagrams for six representative Skyrme models, revealing the microphysical magnetic flux distribution throughout the neutron star core. The phase diagrams are rather complex and the locations of most of the phase transitions can only be determined through numerical calculations. Nonetheless, we find that for all equations of state considered in this work, much of the outer core exhibits type-1.5 superconductivity, rather than type-II superconductivity as is generally assumed. For local magnetic field strengths $lesssim 10^{14} , {rm G}$, the magnetic flux is distributed inhomogeneously, with bundles of magnetic fluxtubes separated by flux-free Meissner regions. We provide an approximate criterion to determine the transition between this type-1.5 phase and the type-I region in the inner core.
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