Road racing shoes have recently evolved to incorporate maximal midsole cushioning and an embedded carbon fibre plate. Shoes in this category have been labelled ‘Advanced Footwear Technology’ (AFT) and may significantly contribute to improvements in running economy, in part due to biomechanical changes at the foot and ankle. However, little is currently known regarding the effect of AFT on common biomechanical risk factors for injury. In addition, most biomechanical research on AFT to date has focused on early prototypes, with less research on more recent versions of these shoes, such as the Nike Vaporfly NEXT%. Therefore, the purpose of this study was to compare lower extremity running biomechanics in the Nike Vaporfly NEXT% (NEXT%) to a minimally cushioned road shoe. Twelve competitive runners ran overground in a laboratory at their current estimated marathon pace while three-dimensional ankle, knee, and hip kinematics and kinetics were collected. Regarding injury-related metrics, eversion excursion was significantly greater in the NEXT% shoe, which has been observed in runners with a history of navicular stress fracture. For performance-related metrics, significantly less peak dorsiflexion and dorsiflexion excursion, as well as a smaller peak plantar flexion moment and lower positive and negative ankle joint work, were found in the NEXT% shoe compared to the minimal shoe. These findings may help biomechanically explain the performance benefits of AFT and support previous research on prototype AFT. However, we also observed a significantly higher peak knee extensor moment in the NEXT% shoe, which was a novel finding and may offset some of the performance benefits seen at the ankle.