We compared how management approaches affected shade tree diversity, soil properties, and provisioning and carbon sequestration ecosystem services in three shade coffee cooperatives. Collectively managed cooperatives utilized less diverse shade, and pruned coffee and shade trees more intensively, than individual farms. Soil properties showed significant differences among the cooperatives, with the following properties contributing to differentiation: N, pH, P, K, and Ca. Higher tree richness was associated with higher soil pH, CEC, Ca, and Mg, and lower K. Higher tree densities were associated with lower N, K, and organic matter. Although we found differences in the incidence of provisioning services (e.g., fruit), all plantations generated products other than coffee. No differences were observed between C-stocks. The history and institutional arrangements of cooperatives can influence management approaches, which affect ecosystem properties and services. Our study corroborates that interdisciplinary investigations are essential to understand the socio-ecological context of tropical shade coffee landscapes.