Background. Simulation-based learning environments are used extensively to support learning in complex business systems. Nevertheless, studies have identified problems and limitations due to cognitive processing difficulties. In particular, previous research has addressed some aspects of model transparency and instructional strategy and produced inconclusive results. Aim. This study investigates the learning effects of using transparent simulations (that is, showing users the internal structure of models) and exploratory guidance (that is, guiding learners so they are able to explore the simulation by themselves, supported by specific cognitive aids) from a mental models perspective. Method. A test based on a simulation experiment with a system dynamics model, representing a supply chain system, was performed. Participants are required to use the simulator to investigate some issues related to the bullwhip effect and other supply chain coordination concepts. Results. Participants provided with the more transparent strategy and offered the more exploratory guidance demonstrated better understanding of the structure and behaviour of the underlying model. However, our results suggest that while exploratory guidance is a beneficial method for understanding both model structure and behaviour, making only the model transparent is more limited in its effect.