We study motivic zeta functions of degenerating families of Calabi-Yau varieties. Our main result says that they satisfy an analog of Igusa's monodromy conjecture if the family has a so-called Galois-equivariant Kulikov model; we provide several classes of examples where this condition is verified. We also establish a close relation between the zeta function and the skeleton that appeared in Kontsevich and Soibelman's non-archimedean interpretation of the SYZ conjecture in mirror symmetry. Comment: New result on existence of Kulikov models for abelian varieties added in section 5.1
