ObjectivesThis study investigated relationships between isometric trunk and hip extensor strength, lumbar muscle morphology, and the risk of hamstring and knee ligament injuries in Australian Football League and National Rugby League players. DesignProspective cohort study. MethodsTrunk and hip extensor strength, multifidus and quadratus lumborum cross-sectional area were measured during the 2020 pre-season. Logistic regressions and decision trees were employed to explore associations between maximum strength, strength endurance, multifidus and quadratus lumborum cross-sectional area, age, previous injuries, and hamstring and knee ligament injury risk. ResultsGreater strength endurance [odds ratio = 0.42 (0.23–0.74), p = 0.004] and maximum strength [odds ratio = 0.55 (0.31–0.94), p = 0.039] reduced hamstring injury risk. Increased risk of knee ligament injuries was associated with larger multifidus [odds ratio = 1.66 (1.14–2.45), p = 0.008] and higher multifidus to quadratus lumborum ratio (odds ratio = 1.57 (1.13–2.23), p = 0.008]. Decision tree models indicated that low strength endurance (< 99 Nm) characterised hamstring strains, while high (≥ 1.33) multifidus to quadratus lumborum ratio mitigated risk. Knee ligament injuries were associated with larger (≥ 8.49 cm2) multifidus, greater (≥ 1.25) multifidus to quadratus lumborum ratio, and lower maximum strength (< 9.24 N/kg). ConclusionsPlayers with lower trunk and hip extensor maximum strength and strength endurance had increased risk of hamstring injuries, while knee ligament injury risk was elevated with larger multifidus cross-sectional area, higher multifidus to quadratus lumborum ratio, and lower maximum trunk and hip extensor strength.