This study examined the effects of minimal and conventional running footwear on medial tibiofemoral cartilage mechanics and longitudinal failure probability. The current investigation examined twenty males who habitually ran in minimal footwear and 20 males who habitually ran in conventional footwear. Kinematic data during overground running were collected using a motion-capture system and ground reaction forces using a force plate. Medial tibiofemoral loading was examined using musculoskeletal simulation and cartilage failure probability via probabilistic modelling. In habitual minimal footwear users, peak medial tibiofemoral cartilage force, stress and strain were significantly greater in conventional (force = 7.43 BW, stress = 5.12 MPa and strain = 0.30), compared to minimal footwear (force = 7.11 BW, stress 4.65 MPa and strain = 0.28), though no significant differences in these parameters were evident in non-habitual minimal footwear users (conventional: force = 7.50 BW, stress = 5.05 MPa and strain = 0.30; minimal: force = 7.40 BW, stress = 4.77 MPa and strain = 0.29). However, in both habitual and non-habitual minimal footwear users, the probability of medial tibiofemoral cartilage failure was significantly greater in conventional (habitual = 47.19% and non-habitual = 50.00%) compared to minimal footwear (habitual = 33.18% and non-habitual = 32.81%) users. The observations from this investigation show that compared to minimal footwear, conventional footwear appears to have a negative influence on medial tibiofemoral cartilage health.