Kostant gave a model for the real geometric quantization associated to polarizations via the cohomology associated to the sheaf of flat sections of a pre-quantum line bundle. This model is well-adapted for real polarizations given by integrable systems and toric manifolds. In the latter case, the cohomology can be computed counting integral points inside the associated Delzant polytope. In this article we extend Kostant’s geometric quantization to semitoric integrable systems and almost toric manifolds. In these cases the dimension of the acting torus is smaller than half of the dimension of the manifold. In particular, we compute the cohomology groups associated to the geometric quantization if the real polarization is the one associated to an integrable system with focus-focus type singularities in dimension four. As application we determine models for the geometric quantization of K3 surfaces, a spin-spin system, the spherical pendulum, and a spin-oscillator system under this scheme.