In this work, we investigate numerically a system of partial differential equations that describes the interactions between populations of predators and preys. The system considers the effects of anomalous diffusion and generalized Michaelis–Menten-type reactions. For the sake of generality, we consider an extended form of that system in various spatial dimensions and propose two finite-difference methods to approximate its solutions. Both methodologies are presented in alternative forms to facilitate their analyses and computer implementations. We show that both schemes are structure-preserving techniques, in the sense that they can keep the positive and bounded character of the computational approximations. This is in agreement with the relevant solutions of the original population model. Moreover, we prove rigorously that the schemes are consistent discretizations of the generalized continuous model and that they are stable and convergent. The methodologies were implemented efficiently using MATLAB. Some computer simulations are provided for illustration purposes. In particular, we use our schemes in the investigation of complex patterns in some two- and three-dimensional predator–prey systems with anomalous diffusion.