Comparative and integrative tools are of fundamental value in ecology for understanding outcomes of biological processes, and making generalizations and predictions. Although ecosystem engineering has been shown to play a fundamental role in community organization, there are no standardized methods to measure such effects. We present a framework and methodology for assessing the impact of physical ecosystem engineers on three general features of community organization: (1) species richness and composition, (2) stability of richness over time, and (3) dominance patterns of species assemblages. We then apply the framework and methodology to assess the effects of the cushion plant Azorella monantha on high-Andean plant communities on two mountaintops. Substrate temperatures, soil moisture and the availability of mineral nutrient resources were compared between A. monantha and surrounding open areas to ascertain whether cushions altered abiotic environmental conditions, while community analysis assessed changes in species richness, composition and abundances at patch and landscape levels. Cushions thermally buffered temperature extremes and increased soil moisture, but had no detectable effect on soil mineral nutrients. Cushion habitat was not more species rich than surrounding areas, but cushions added new species into the community, altering species composition and markedly enhancing landscape-level richness. Cushions also showed potential for stabilizing species richness over time, and changed patterns of species dominance. Findings were consistent across mountaintops. We evaluate the general utility of the framework and call for its application in other systems as a means to generate comparative data sets for assessing the general effects of ecosystem engineers on community organization.