Successful locomotion through complex, heterogeneous environments requires the muscles that power locomotion to function effectively under a wide variety of conditions. Although considerable data exist on how animals modulate both kinematics and motor pattern when confronted with orientation (i.e. incline) demands, little is known about the modulation of muscle function in response to changes in structural demands like substrate diameter, compliance and texture. Here, we used high-speed videography and electromyography to examine how substrate incline and perch diameter affected the kinematics and muscle function of both the forelimb and hindlimb in the green anole (Anolis carolinensis). Surprisingly, we found a decoupling of the modulation of kinematics and motor activity, with kinematics being more affected by perch diameter than by incline, and muscle function being more affected by incline than by perch diameter. Also, muscle activity was most stereotyped on the broad, vertical condition, suggesting that, despite being classified as a trunk-crown ecomorph, this species may prefer trunks. These data emphasize the complex interactions between the processes that underlie animal movement and the importance of examining muscle function when considering both the evolution of locomotion and the impacts of ecology on function.