The depth-dependent, as-grown and deformation-induced strain and dislocations partitioned through the interfaces in a two-phase layered NiAl–Cr(Mo) structure are directly measured at the mesoscale using 3-D X-ray microdiffraction. It is demonstrated that in the as-grown, undeformed state, neighboring submicron Cr solid solution and NiAl eutectic lamellae (doped with ∼3% Mo) form a heterointerface with 180° rotation around a 〈112〉 pole. It is shown that the mechanical response to the indentation of a layered composite with alternating Cr(Mo)–NiAl lamellae is distinct from the response of single-phase materials. In the center of the indent, after the load is released, the NiAl lamellae are under compressive forward stresses (with the same sign as the indentation-induced compression) while Cr solid solution lamellae are under tensile back stresses (with opposite sign from the indentation load). The depth-dependent alternation of compressive/tensile residual strains in the neighboring Cr solid solution and NiAl lamellae is understood in the framework of the Mughrabi’s composite model considering two types of structure elements: harder and softer regions. Under indentation, both kinds of lamellae are assumed to deform compatibly. After the load is released, residual forward stresses are formed in the harder lamellae, and back stresses are formed in the mechanically softer lamellae. Line-broadening analysis of the intensity distribution along the diffraction vector reveals a 15-times increase in dislocation density in the near-surface zone in the center of the indent. Such a large increase is typical for severe deformation.