Abstract Background Patients with lower extremity amputation frequently suffer from socket-related problems. This seriously limits prosthesis use, level of activity and health-related quality of life (HRQoL). An additional problem in patients with lower extremity amputation are asymmetries in gait kinematics possibly accounting for back pain. Bone-anchored prostheses (BAPs) are a possible solution for socket-related problems. Knowledge concerning the level of function, activity and HRQoL after surgery is limited. The aims of this ongoing study are to: a) describe changes in the level of function, activity, HRQoL and satisfaction over time compared to baseline before surgery; b) examine potential predictors for changes in kinematics, prosthetic use, walking ability, HRQoL, prosthesis comfort over time and level of stump pain at follow-up; c) examine potential mechanisms for change of back pain over time by identifying determinants, moderators and mediators. Methods/design A prospective 5-year longitudinal study with multiple follow-ups. All adults, between May 2014 and May 2018, with lower extremity amputation receiving a press-fit BAP are enrolled consecutively. Patients with socket-related problems and trauma, tumour resection or stable vascular disease as cause of primary amputation will be included. Exclusion criteria are severe cognitive or psychiatric disorders. Follow-ups are planned at six-months, one-, two- and five-years after BAP surgery. The main study outcomes follow, in part, the ICF classification: a) level of function defined as kinematics in coronal plane, hip abductor strength, prosthetic use, back pain and stump pain; b) level of activity defined as mobility level and walking ability; c) HRQoL; d) satisfaction defined as prosthesis comfort and global perceived effect. Changes over time for the continuous outcomes and the dichotomized outcome (back pain) will be analysed using generalised estimating equations (GEE). Multivariate GEE will be used to identify potential predictors for change of coronal plane kinematics, prosthetic use, walking ability, HRQoL, prosthesis comfort and for the level of post-operative stump pain. Finally, potential mechanisms for change in back pain frequency will be explored using coronal plane kinematics as a potential determinant, stump pain as moderator and hip abductor strength as mediator. Discussion This study may identify predictors for clinically relevant outcome measures. Trial registration NTR5776 . Registered 11 March 2016, retrospectively registered.