Shahid Naeem studies the ecological and environmental consequences of biodiversity loss. He is interested in how changes in the distribution and abundance of plants, animals, and microbes, affect how ecosystems function and, by extension, how ecosystems services are affected. His work combines theoretical, observational, and experimental studies under field and laboratory conditions, to uncover the mechanistic bases for the impacts of biodiversity loss on ecosystems. His work has demonstrated how the loss of species from ecosystems affect their ability to resist invasion by other species, affect production and nutrient cycling, and affect the reliability and stability of ecosystems. He is actively involved in bringing the science of biodiversity and ecosystem functioning to conservation, restoration, and policy development.