This review focuses on materials and methods used to induce phenotypic changes in macrophages and fibroblasts. Herein, we give a brief overview on how changes in macrophages and fibroblasts phenotypes are critical biomarkers for identification of implant acceptance, wound healing effectiveness, and are also essential for evaluating the regenerative capabilities of some hybrid strategies that involve the combination of natural and synthetic materials. The different types of cells present during the host response have been extensively studied for evaluating the reaction to different materials and there are varied material approaches towards fabrication of biocompatible substrates. We discuss how natural and synthetic materials have been used to engineer desirable outcomes in lung, heart, liver, skin, and musculoskeletal implants, and how certain properties such as rigidity, surface shape, and porosity play key roles in the progression of the host response. Several fabrication strategies are discussed to control the phenotype of infiltrating macrophages and fibroblasts: decellularization of scaffolds, surface coatings, implant shape, and pore size apart from biochemical signaling pathways that can inhibit or accelerate unfavorable host responses. It is essential to factor all the different design principles and material fabrication criteria for evaluating the choice of implant materials or regenerative therapeutic strategies.