This study presents a description of the new technology for producing external or internal layers made of different powders mixed with epoxy resin, which can perform various functions as a protection against impact, erosion, or elevated temperatures as well as provide interlayers during the manufacturing of a ceramic protective barrier by air plasma spraying (APS) on the PMC substrate made of carbon–epoxy. Six types of powders (copper, quartz sand, Al2O3, aluminum, crystalline silica, and microballoon) were used to manufacture (120 °C) different kinds of protective layers (PLs), perfectly joined with the PMCs, in one single autoclave process. The two-layered specimens (2 × 25 × 110 mm) were subjected to a three-point bending (3-PB) displacement-controlled deformation process to determine the critical values of deformations at which the PLs can work safely without being cracked or delaminated. The tests were performed up to the final failure, observing various damage and cracking phenomena. Finally, the numerical simulations were carried out using the representative volume element (RVE) model of the most efforted central parts of the samples to determine the effect of powder grain diameter and resin content on the elastic properties and damage growth of the newly proposed multifunctional PLs. The stress concentrations and damage processes, including cracking and delamination, were analyzed in the whole two-layered system. The best result, in terms of strength during 3-PB testing, was achieved with the PL made of aluminum powder.