Dynamical reaction–diffusion processes and metapopulation models are standard modelling approaches for a wide array of phenomena in which local quantities—such as density, potentials and particles—diffuse and interact according to the physical laws. Here, we study the behaviour of the basic reaction–diffusion process (given by the reaction steps B¿A and B+A¿2B) defined on networks with heterogeneous topology and no limit on the nodes’ occupation number. We investigate the effect of network topology on the basic properties of the system’s phase diagram and find that the network heterogeneity sustains the reaction activity even in the limit of a vanishing density of particles, eventually suppressing the critical point in density-driven phase transitions, whereas phase transition and critical points independent of the particle density are not altered by topological fluctuations. This work lays out a theoretical and computational microscopic framework for the study of a wide range of realistic metapopulation and agent-based models that include the complex features of real-world networks.