Recently isolated populations offer a good biological model to infer the evolutionary forces responsible for the current divergences across populations. We coupled genetic, morphometric, ecological, and demographic analyses from three island populations of the endemic Balearic Wall Lizard, Podarcis lilfordi, (Balearic archipelago, Spain) to infer the mechanisms underlying the observed differences in body size. For each population, we described plant community structure, derived a biotic capacity index, and used individual-based data on 1369 lizards captured and released during 6 yr (2009–2015) to estimate population density and body growth patterns. We used genetic data collected on 80 individuals (∼27 for each population) to infer genetic divergences across islets and population history. Body size divergences cannot be explained by the ecological or population characteristics. Individual growth was slower in the smallest island, where lizards reached the largest average body size. In addition to having the highest density, results suggested that resource availability does not constrain asymptotic body size, but the speed at which individuals reach it does. The Approximate Bayesian Computation used to infer population history from genetic data supported the occurrence of two bottlenecks in the islet with the highest anthropogenic footprint. We emphasize the need to integrate ecological and genetic data and the importance of considering the effects of past human disturbance as an additional force in being able to model present island fauna.