We study the interplay between the Fourier-Mukai transform and the decomposition theorem for an integrable system π : M → B. Our main conjecture is that the Fourier-Mukai transform of sheaves of Kähler differentials, after restriction to the formal neighborhood of the zero section, are quantized by the Hodge modules arising in the decomposition theorem for π. For an integrable system, our formulation unifies the Fourier-Mukai calculation of the structure sheaf by Arinkin-Fedorov, the theorem of the higher direct images by Matsushita, and the "perverse = Hodge" identity by the second and the third authors.As evidence, we show that these Fourier-Mukai images are Cohen-Macaulay sheaves with middle-dimensional support on the relative Picard space, with support governed by the higher discriminants of the integrable system. We also prove the conjecture for smooth integrable systems and certain 2-dimensional families with nodal singular fibers. Finally, we sketch the proof when cuspidal fibers appear.