This study explores the proposed affordances and limitations of the substance metaphor for energy in the context of a computer simulation that illustrates processes of energy transfer and transformation. We examine data from eight interviews conducted with introductory physics students as they used the simulation. We empirically explore the hypotheses that (i) student and (ii) instructional use of the substance metaphor promote specific affordances, such as energy conservation, transfer, and localization, and specific limitations, such as locating potential energy in a single object and appropriating material qualities to energy. We find that the frequency of both affordances and limitations increases when the simulation embeds an explicit substance metaphor and that the affordances and limitations more often co-occur with students' substance metaphor use. However, in all cases, the number of instances of affordances is greater than that of limitations, which suggests that the substance metaphor is beneficial to instruction and student discourse.