End-to-side anastomoses are commonly utilised in peripheral arterial bypass surgery and are plagued by high rates of re-stenosis which are contributed to by non-physiological blood flow impacting the arterial and graft structures. Computational simulations can examine how patient-specific surgical decisions in bypass graft placement and material selection affect blood flow and future risk of graft restenosis. Despite graft geometry and compliance being key predictors of restenosis, current simulations of femoro-popliteal artery grafts do not consider the interaction of flowing blood with compliant vessel, graft, and suture structures. Utilising fluid–structure interaction simulations, this study examines the impact of surgical technique, such as anastomosis angle, graft material, and suture material, on blood flow and fluid–structure forces in patient-specific asymptomatic arterial tree versus side-to-end peripheral grafts for symptomatic atherosclerotic disease. To render these complex simulations numerically feasible, our pipeline uses regional suture mechanics and a pre-stress pipeline previously validated in small-scale idealised models. Our simulations found that higher anastomosis angles generate larger regions of slow and recirculating blood, characterised by non-physiologically low shear stress and high oscillatory shear index. The use of compliant graft materials reduces regions of non-physiologically high shear stress only when used in combination with compliant suture materials. Altogether, our fluid–structure interaction simulation provides patient-specific platforms for vascular surgery decisions concerning graft geometry and material.