Fundamental changes in the societal use of biophysical resources are required for a sustainability transformation. Current socioeconomic metabolism research traces flows of energy, materials or substances to capture resource use: input of raw materials or energy, their fate in production and consumption, and the discharge of wastes and emissions. This approach has yielded important insights into eco-efficiency and long-term drivers of resource use. But socio-metabolic research has not yet fully incorporated material stocks or their services, hence not completely exploiting the analytic power of the metabolism concept. This commentary argues for a material stock–flow–service nexus approach focused on the analysis of interrelations between material and energy flows, socioeconomic material stocks (“in-use stocks of materials”) and the services provided by specific stock/flow combinations. Analyzing the interrelations between stocks, flows and services will allow researchers to develop highly innovative indicators of eco-efficiency and open new research directions that will help to better understand biophysical foundations of transformations towards sustainability.