Abstract This article experimentally demonstrates a novel, microgrid control algorithm based on a two-layer economic model predictive control framework that was previously developed by the authors. This algorithm is applied to an isolated microgrid with a solar photovoltaic system, a battery bank and a gasoline-fuelled generator. The control system performance is experimentally compared to a baseline algorithm over 5 min and 10 h periods, while an experimentally validated model is used to compare performance over a full year. The results indicate that applying the proposed, two-layer economic model predictive control algorithm can reduce operating costs and CO 2 emissions by 5%–10% relative to conventional, rule based methods, and by 10%–15% if improved solar and demand forecasts are available. Furthermore, the proposed two-level algorithm can achieve reductions of up to 5% compared with current state-of-the-art methods which only attempt to optimize performance in the energy management system.