Dark matter (DM)-electron scattering is a prime target of a number of direct DM detection experiments and constitutes a promising avenue for exploring interactions of DM in the sub-GeV mass-range, challenging to probe with nuclear recoils. We extend the recently proposed halo-independent analysis method for DM-electron scattering, which allows to infer the local DM halo properties without any additional assumptions about them, to include in-medium effects through dielectric functions of the target material. We show that in-medium effects could significantly affect halo-independent analysis response functions for germanium and silicon and thus are essential for proper inference of local DM halo characteristics from direct DM detection data.