Composite soft materials are used as compounds for determining the effects of mechanical cues on cell behavior and cell encapsulation and for controlling drug release. The appropriate composite soft materials are conventionally prepared by selective deposition of polymers at the surface of an ionic hydrogel. In the present study we address the impact of a mechanically stratified two-layer structure of these materials on their overall mechanical characterization by applying a combination of nanoindentation, confocal microscopy and finite element modelling. We prepare covalent cross-linked hydrogels based on acrylamide (AAM) and including an anionic group, and impregnate them using a multilayer deposition strategy of alternating exposure to cationic chitosan and anionic alginate. The thickness of the chitosan–alginate layer on the hydrogels was determined to be 0.4 ± 0.05 μm for 4 bilayers, and 0.7 ± 0.1 μm for the 8 bilayer deposition procedure employing a fluorescently labelled chitosan and confocal microscopy. The force–indentation data for the AAM gels were highly reproducible, whereas 77% and 50% of the force–indentation data were reproducible following the 4 and 8 bilayer deposition. The main trends in the reproducible force–distance data were found to yield an apparent increased Young's modulus after the deposition. Finite element modelling showed that adaption of a homogeneous Young's modulus for the specimens with deposited layers yields approximately three times too low stiffness compared to the estimate of the mechanical properties of the outer part in the two-layered mechanical model. The thickness of the multilayer region determined by confocal microscopy was used in the model. This study shows that the mechanical layered property needs to be included in the interpretation of the nanoindentation data when there is a significant mechanical contrast.