To characterize how moderately large impactors might alter the differentiation and internal structure of Mars, we examine the fractional crystallization of intermediate depth magma oceans, and document that residual liquids ultimately become denser than normal Martian mantle, establishing unstable density gradients and inducing extensive magma descent within an evolving Mars. Fractional crystallization of intermediate depth magma oceans on Mars is likely to produce liquids that are dense enough to descend to the core-mantle boundary (CMB) and thus form a stably stratified thermochemical boundary layer at the Martian CMB. If this layer cooled sufficiently to crystallize, its mineralogy would be dominated by garnet and ferropericlase, or stishovite and ringwoodite, with changes in the descending liquid’s bulk composition having relatively minor effects on the resulting phase assemblage. While the size of Mars’ core remains uncertain, the addition of such a thermal boundary layer would impede the stabilization of (Mg, Fe)SiO3-perovskite at depth in Mars, although it would contain modest amounts of CaSiO3-perovskite. Such a compositionally distinct thermal boundary layer at the base of the Martian mantle would substantially elevate the inferred temperature of the Martian core, and also produce markedly lowered heat flow at the top of its core, with a potentially causal relation with the current lack of an internally generated Martian magnetic field. We calculate the seismic velocity anomalies that would be expected to be associated with such a layer, and find that the shift in mineralogy at depth should produce a seismic discontinuity that could prospectively be detectable by Martian seismic deployments.