Anomalous transport in equilibrium fermionic fluids chirally coupled to background Weyl-type nonmetricity is studied. A formal descent analysis is carried out in which the dependence of the anomaly polynomial on the nonmetricity tensor is encoded in a Weyl invariant four-form. The constitutive relation of the axial-vector current is evaluated from the equilibrium partition function obtained using transgression techniques, showing the existence of nonmetricity-mediated chiral separation effects driven by the fluid’s vorticity and the Weyl magnetic field. A second nonminimal coupling of fermionic matter to metric-affine geometries proposed in the literature is also discussed.