We construct charged black branes in type IIA flux compactifications that are dual to (2+1)-dimensional field theories at finite density. The internal space is a general Calabi-Yau manifold with fluxes, with internal dimensions much smaller than the AdS radius. Gauge fields descend from the 3-form RR potential evaluated on harmonic forms of the Calabi-Yau, and Kaluza-Klein modes decouple. Black branes are described by a four-dimensional effective field theory that includes only a few light fields and is valid over a parametrically large range of scales. This effective theory determines the low energy dynamics, stability and thermodynamic properties. Tools from flux compactifications are also used to construct holographic CFTs with no relevant scalar operators, that can lead to symmetric phases of condensed matter systems stable to very low temperatures. The general formalism is illustrated with simple examples such as toroidal compactifications and manifolds with a single size modulus. We initiate the classification of holographic phases of matter described by flux compactifications, which include generalized Reissner-Nordstrom branes, nonsupersymmetric $AdS_2 \times R^2$ and hyperscaling violating solutions. Show Partial Abstract