In 1993 Keski-Vakkuri and Wen introduced a model for the fractional quantum Hall effect based on multilayer two-dimensional electron systems satisfying quasi-periodic boundary conditions. Such a model is essentially specified by a choice of a complex torus E and a symmetric positively definite matrix K of size g with non-negative integral coefficients, satisfying some further constraints. The space of the corresponding wave functions turns out to be \(\delta \)-dimensional, where \(\delta \) is the determinant of K. We construct a hermitian holomorphic bundle of rank \(\delta \) on the abelian variety A (which is the g-fold product of the torus E with itself), whose fibres can be identified with the space of wave function of Keski-Vakkuri and Wen. A rigorous construction of this “magnetic bundle” involves the technique of Fourier–Mukai transforms on abelian varieties. The constructed bundle turns out to be simple and semi-homogeneous and it can be equipped with two different (and natural) hermitian metrics: the one coming from the center-of-mass dynamics and the one coming from the Hilbert space of the underlying many-body system. We prove that the canonical Bott–Chern connection of the first hermitian metric is always projectively flat and give sufficient conditions for this property for the second hermitian metric.