IntroductionThere is a limited research exploring biomechanical risk factors for the development of knee osteoarthritis (KOA) and lower back pain (LBP) between lower limb amputee subgroups, (eg, transtibial amputees (TTA) vs transfemoral amputees (TFA), or TTA dysvascular vs TTA traumatic). Previous reviews have focused primarily on studies where symptoms of KOA or LBP are present, however, due to limited study numbers, this hinders their scope and ability to compare between amputee subgroups. Therefore, the aim of this systematic review is to descriptively compare biomechanical risk factors for developing KOA and LBP between lower limb amputee subgroups, irrespective of whether KOA or LBP was present.Methods and analysisThis review is currently in progress and screening results are presented alongside the protocol to highlight challenges encountered during data extraction. Five electronic databases were searched (Medline—Web of Science, PubMed, CINAHL, Embase and Scopus). Eligible studies were observational or interventional, reporting biomechanical gait outcomes for individual legs in adult lower limb amputees during flat walking, incline/decline walking or stair ascent/descent. Two reviewers screened for eligibility and level of agreement was assessed using Cohen’s Kappa. Data extraction is ongoing. Risk of bias will be assessed using a modified Downs and Black method, and outcome measures will be descriptively synthesised.Ethics and disseminationThere are no ethical considerations for this systematic review. Due to its scope, results are expected to be published in three separate manuscripts: (1) biomechanical risk factors of KOA between TTA and TFA, relative to non-amputees, (2) biomechanical risk factors of LBP between TTA and TFA, relative to non-amputees and (3) biomechanical risk factors of KOA and LBP between TTA with traumatic or dysvascular causes, relative to non-amputees.PROSPERO registration numberCRD42020158247.