Background: Most running biomechanics studies have focused on either the patellofemoral joint (PFJ) or Achilles tendon (AT) alone, generating fragmented understanding of how these structures interact as components of an integrated kinetic chain during running. This study was to investigate concurrent biomechanical changes in the PFJ and AT in recreational runners. Methods: The recreational runners who are accustomed to run with rearfoot strike (RFS, n = 15) and forefoot strike (FFS, n = 15) patterns were recruited. They were instructed to run at 10 km/h in cushion shoes with their habitual strike patterns on an instrumented split-belt treadmill. Kinematics of the ankle and knee joints in the sagittal plane and ground reaction forces were recorded simultaneously. The contact force and stress at the PFJ, as well as the force, loading rate, impulse, and stress of the AT, were calculated. Results: The habitual RFS runners had significantly higher peak extension moment (p = 0.019, ES = 0.906), peak quadriceps force (p = 0.010, ES = 1.008), PFJ contact force (p = 0.007, ES = 1.056) and stress (p = 0.042, ES = 0.958) than habitual FFS runners. The peak plantar flexion moment (p < 0.001, ES = 2.692), peak AT force (p < 0.001, ES = -1.788), average (p < 0.001, ES = -2.337) and peak AT loading rate (p < 0.001, ES =-1.996), AT impulse (p = 0.002, ES = -1.246) and stress (p = 0.006, ES = -1.082) of the habitual RFS runners were significantly lower than those of the habitual FFS runners. Conclusion: The FFS pattern could decrease PFJ load but simultaneously increased the mechanical load on the AT. Conversely, the RFS pattern increased PFJ load, but imposed less load on the AT.