Presently, developments in weightbearing computed tomography and biplanar fluoroscopy technologies offer exciting avenues for investigating normative and pathologic foot function with increasing precision. Still, data quantifying sesamoid bone and proximal phalange motion are currently sparse. To express joint kinematics and compare various clinical cohorts, future studies of first ray motion will necessitate robust coordinate frames that respect the variations in underlying anatomy while also aligning closely with the functional, physiological axes of motion. These activity-dependent functional axes may be represented by a mean helical axis of the joint motion. Our cadaveric study quantified joint kinematics from weightbearing computed tomography scans during simulated toe lift and heel rise tasks. We compared the spatial orientations of the mean finite helical axes of the metatarsosesamoidal and metatarsophalangeal joints to the primary joint axis of two relevant methods for defining metatarsal coordinate frames: inertial axes and fitting of geometric primitives. The resultant kinematics exhibited less crosstalk when using a metatarsal coordinate system based on fitting cylindrical primitives to the bony anatomy compared to using principal component axes. Respective metatarsophalangeal and metatarsosesamoidal arthrokinematic contact paths and instantaneous centers of rotation were similar between activities and agree well with currently published data. This study outlines a methodology for quantitatively assessing the efficacy and utility of various anatomical joint coordinate system definitions. Improvements in our ability to characterize the shape and motion of foot bones in the context of functional tasks will elucidate their biomechanical roles and aid clinicians in refining treatment strategies.