Oceanic islands are not static entities; instead, their size and features change dynamically through time, a process called island ontogeny. It has been hypothesized that the gradual or at times abrupt changes an island experiences during its lifespan can have a strong effect on the composition and evolution of biological communities. The general dynamic model of island biogeography assumes that island area and topographic complexity change through time and influence the number of available niches, and thus rates of diversification. A previous study demonstrated the role of single-island ontogeny on the Hawaiian biota, but most diversification studies on islands have not considered it. We tested under what conditions island ontogeny can bias diversification studies if not taken into account, using a simulation approach based on an extended version of the phylogenetic framework DAISIE. We simulated evolution on islands subject to ontogenetic processes and attempted to infer the generating parameters using existing methods that ignore ontogeny. Furthermore, we assessed how reasonable predictions of future biodiversity that ignore past island ontogeny are. Our analyses allow us to lay out guidelines on how and when to incorporate island geomorphological data into island phylogenetic diversification studies. This will lead to more robust conclusions about the origin and maintenance of biodiversity on oceanic islands.