Fine particulate matter (PM2.5) is associated with various adverse health outcomes and poses serious concerns for public health. However, ground monitoring stations for PM2.5 measurements are mostly installed in population-dense or urban areas. Thus, satellite retrieved aerosol optical depth (AOD) data, which provide spatial and temporal surrogates of exposure, have become an important tool for PM2.5 estimates in a study area. In this study, we used AOD estimates of surface PM2.5 together with meteorological and land use variables to estimate monthly PM2.5 concentrations at a spatial resolution of 3 km2 over Taiwan Island from 2015 to 2019. An ensemble two-stage estimation procedure was proposed, with a generalized additive model (GAM) for temporal-trend removal in the first stage and a random forest model used to assess residual spatiotemporal variations in the second stage. We obtained a model-fitting R2 of 0.98 with a root mean square error (RMSE) of 1.40 μg/m3. The leave-one-out cross-validation (LOOCV) R2 with seasonal stratification was 0.82, and the RMSE was 3.85 μg/m3, whereas the R2 and RMSE obtained by using the pure random forest approach produced R2 and RMSE values of 0.74 and 4.60 μg/m3, respectively. The results indicated that the ensemble modeling approach had a higher predictive ability than the pure machine learning method and could provide reliable PM2.5 estimates over the entire island, which has complex terrain in terms of land use and topography.