An inverted mass hierarchy in the squark sector, as in so-called "natural supersymmetry", requires non-universal boundary conditions at the mediation scale of SUSY breaking. In this talk I will present a formalism to define such boundary conditions in a basis-independent manner, and apply it to natural SUSY scenarios with a high mediation scale. I will show that many generic scenarios with inverted squark mass hierarchies are in fact minimally flavour violating, or run towards a minimally flavour violating structure at low energies, and thus automatically evade flavour physics constraints.