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Functional outcomes, such as joint flexion and gait, are important indicators of efficacy in musculoskeletal research. Current technologies that objectively assess these parameters, including visual tracking systems and force plates, are challenging to deploy in long-term translational and clinical studies. To that end, we developed a wearable device that measures both physical activity and joint flexion using a single integrated sensor and magnet system, and hypothesized that it could evaluate post-operative functional recovery in an unsupervised setting. To demonstrate the feasibility of measuring joint flexion, we first compared knee motion from the wearable device to that acquired from a motion capture system to confirm that knee flexion measurements during normal human gait, predicted via changes in magnetic field strength, closely correlated with data acquired by motion capture. Using this system, we then monitored a porcine cohort after bilateral stifle arthrotomy to investigate longitudinal changes in physical activity and joint flexion. We found that unsupervised activity declined immediately after surgery, with a return to pre-operative activity occurring over a period of 2 weeks. By providing objective, individualized data on locomotion and joint function, this magnet-based system will facilitate the in vivo assessment of novel therapeutics in orthopaedic research.