Ecological studies strive to identify factors that explain patterns of species distribution and abundance. In lizards, competition and predation are major forces influencing distribution and abundance, but there is also increasing evidence pointing at the influence of habitat structure and prey abundance. Our work explored the latter further by quantifying the effects of vegetation and prey abundance on occupancy and abundance (i.e., estimated probability of detecting more than two individuals) of two sympatrically occurring species in the northern karst belt of Puerto Rico. We hypothesized that Anolis cristatellus would occur in trunk–ground substrates and Anolis krugi on grass–bush substrates according to their ecomorphological classification. We also hypothesized that prey abundance, a component of habitat quality, would have a positive and strong effect on occupancy and abundance. Anolis cristatellus exhibited high occupancy rates (>0.80), influenced by mid-story tree size. A. cristatellus abundance fluctuated over time, with highest probability of detecting two or more individuals in January–March and July–September when prey abundance transitioned from low to high levels. Occupancy of A. krugi was positively influenced by sapling density and prey abundance. Prey abundance exerted a stronger influence on occupancy, but its influence on abundance was negative and strong. Biological interactions and the type of understory substrates may explain the negative relationship. Our study supported predicted relationships between ecomorphology and habitat, but also showed that higher prey abundance may not always translate to higher local abundance. We shed light on these interactions, knowledge needed to advance anole conservation in the advent of land use and climate change.