The indentation of coated systems allows the analysis of the mechanical properties of each individual constituent, or of the entire system, including material constitutive behavior and failure properties. Due to the progressive loading and unloading of the indentation cycle, both cohesive and adhesive failures can occur in the coating and at the coating/substrate interface, respectively. In this work, the Finite Element Method (FEM) was applied to develop a numerical model based on a spherical rigid indenter in contact with a coated compliant substrate. The coating behavior was defined based on the properties of brittle pure elastic materials, while the substrate was assumed elastic-perfectly plastic. Both cohesive and adhesive failure models were included in the analyses, allowing the evaluation of failure in the coating and/or at the coating/substrate interface. The eXtended Finite Element Method (XFEM) was applied to reproduce the cohesive cracks through the coating thickness, while the Cohesive Zone Model (CZM) was used to evaluate the coating/substrate interfacial crack. System failure was analyzed considering a range of coating parameters (elastic modulus, fracture toughness, energy release rate for cohesive propagation, thickness and residual stresses), coating/substrate interface properties (interface toughness and adhesive crack energy release rate) and the radius of the spherical indenter. The range of input values resulted in simulations with cohesive and/or adhesive failures and allowed determination of a parameter that presented good correlation with the occurrence of crack propagation and failure. Cohesive failures in the coating also produced signatures on the load–displacement (P–h) indentation curves, which allowed the evaluation of coating fracture toughness with good agreement with the input toughness values in cases where the coating was thin.