By using adhesion, geckos can move through incredibly challenging habitats. However, continually changing terrain may necessitate modulation of the adhesive apparatus in order to maximize its effectiveness over a range of challenges. Behaviorally modulating how the adhesive system is applied can occur by altering the alignment of the foot relative to the long axis of the body and/or the angles between the digits (interdigital angle). Given the directionality of the adhesive system, geckos likely vary the application of the system via these mechanisms as they run. We quantified 3D movements (using high-speed video) of the day gecko, Phelsuma madagascariensis, running on a range of ecologically relevant inclines (0°, 45°, 90°) and perch diameters (1.5 cm, 10 cm and broad). We measured the instantaneous sum of interdigital angles and foot alignment relative to the body, as well as other kinematic variables, throughout each stride and across treatments. Modulation of foot alignment at 45° and 90° was similar between the forelimb and hind limb, but differed at 0°, suggesting that P. madagascariensis is able to exert an adhesive force using multiple strategies. Both the sum of interdigital angles and alignment in the fore- and hind foot were modulated. Differences in modulation between the limbs are likely related to the underlying morphology. The modulation of interdigital angle and foot alignment suggests that aspects other than the mechanism of adhesion, such as joint morphology, are important for arboreal movement in geckos. Our study of foot usage in arboreal locomotion reveals patterns that may be widespread across pad-bearing lizards. In addition to understanding the constraints exerted by the adhesive apparatus, we highlight how biomechanical traits may respond to the evolution of novel adaptations and morphologies.