The skin is a combination of two different types of tissue—epithelial and connective (mesenchymal). The outer protective layer of the skin, the epidermis, consists of multiple layers of keratinocytes residing on the basement membrane that separates them from the underlying dermis, which consists of a well-vascularized fibrous extracellular matrix seeded mainly by fibroblasts and mesenchymal stromal cells. These skin features suggest that the development of a fibroblast-friendly porous scaffold covered with a flat dense sheath mimicking the basement membrane, and sufficient to support keratinocyte attachment, would be a reasonable approach in the generation of clinically-relevant skin substitutes useful for reconstructive dermatology and burn treatment. Therefore, we developed a procedure to obtain biocompatible composite bilayer scaffolds comprising a spongy dermis-like body (supporting vascularization and appropriate fibroblast and multipotent stromal cell activity) fused with a film-like cover (supporting keratinocyte attachment, growth and differentiation). The sodium alginate (SA), an algae-derived biopolymer, has been used as a base component for these scaffolds while collagen (CL) and fibrinogen (FG) were used as minor additives in variable concentrations. The slow rates of composite SA-based scaffold biodegradation were achieved by using Ba2+ as cross-linking cations. By manipulating the SA/CL/FG ratio we managed to obtain sponge scaffolds with highly interconnected porous structures, with an average pore size ranging from 60 to 300 μm, and sufficient tensile strength (3.12–5.26 MPa). The scaffolds biocompatibility with the major human skin cell types was confirmed by seeding the scaffold sponge compartment with primary skin fibroblasts and subcutaneous adipose-derived stromal cells while the film side biocompatibility was tested using primary human keratinocytes. The obtained results have shown that bilayer alginate-based scaffolds have biological and mechanical properties comparable with CL scaffolds but surpass them in cost efficiency and vascularization ability in the subcutaneous implantation model in laboratory mice.