There is a growing demand for biocompatible and mechanically robust arrays of microcompartments loaded with minute amounts of active substances for sensing or controlled release applications. Here we report on a novel biocompatible composite material, protein – polyphenol – clay (PPC) multilayer film. The material is shown to be strong enough to make robust microchambers retaining the shape and dimensions of truncated square pyramids. We study the mechanical properties and biocompatibility of the PPC microchambers and compare them to those made of synthetic polyelectrolyte multilayer film, poly(styrene sulfonate) – poly(allylammonium) (PSS-PAH). The mechanical properties of the microchambers were characterised under uniaxial compression using nanoindentation with a flat-punch tip. The effective Young’s modulus of PPC microchambers, 166 ± 53 MPa, is found to be lower than that of PSS-PAH microchambers, 245 ± 52 MPa. However, the capacity to elastically absorb the energy of the former, 2.4 ± 1.0 MPa, is marginally higher than of the latter, 2.0 ± 1.3 MPa. Arrays of microchambers were sealed onto a polyethylene film, loaded with a model oil-soluble drug, and their biocompatibility was tested using an ex vivo 3D human skin reconstruct model. We found no evidence for toxicity with the PPC microchambers; however, PSS-PAH microchambers stimulated reduced cell density in the epidermis and significantly affected epidermal-dermal attachment. Both materials do not alter skin cell proliferation but affect skin cell differentiation. We interpret that rather than affecting epidermal barrier function, these data suggest the applied plastic films with microchamber arrays affect transpiration, normoxia and moisture exchange.