Regenerated secondary forests in the tropics are resilient ecosystems. Differences in land-use history and disturbance, abiotic and biotic site conditions, and successional pathways can influence secondary forest biodiversity, structure, ecological functions, and ecosystem services. However, studies assessing the supply of ecosystem services of secondary forests are limited. We examined trees in plots located across late successional stage secondary forest in the Luquillo Experimental Forest, Puerto Rico with three combinations of historical canopy cover (circa 1936) and post-agricultural recovery pathways: (1) > 50% canopy cover and passive regeneration (>50 P), (2) < 50% canopy cover and passive regeneration (<50 P), and (3) < 50% canopy cover and assisted + passive regeneration (<50 A+P). Using i-Tree Eco methodology, we investigated if differences in historical cover and passive vs assisted natural regeneration resulted in differences in composition and structure, hydrological functions, and estimated regulating ecosystem services, and compared the results between native and non-native species. The <50 P plots had greater species richness than the >50 P and <50 A+P plots, while the <50 A+P plots had significantly greater DBH, height, basal area, aboveground biomass, and estimated quantities of evaporation and transpiration, carbon storage, and removal of airborne contaminants compared to the other recovery pathways. Differences among plot groups can be attributed to historical management actions in concert with successional trajectories characteristic of novel secondary forests. Native species dominated throughout these secondary forests and cumulatively exhibited services that were 1.3 to 3.5 times greater than those of non-native species. However, non-native trees contributed disproportionally to basal area and aboveground biomass, and thus to some ecosystem services. Both natives and non-natives exhibited service provision that varied significantly with diameter size class and service type, and large trees were observed to be dominant service providers irrespective of species origin. Our study marks the first landscape-scale quantitative assessment of forest composition, structure and ecological functioning that is explicitly linked to exploring regulating ecosystem services within the montane secondary forest in Puerto Rico and expands representation of this research from the Caribbean. The findings underscore the role of historical land use and recovery pathways in driving services of tropical forests and show how ecosystem functions can vary in accordance with dynamic structural attributes of individual trees. This research can provide a useful point of comparison for analysis of biomass accumulation, ecosystem service provision, and evaluating service tradeoffs associated with forest structure in other recovering and old-growth tropical landscapes.