Hughes missed the 2016 Olympic Games in Rio due to a tear in his right knee ligament, sustained in a fall earlier in the season. He competed at the 2016 British Athletics Championships against doctor's warnings, but could only manage fourth. He also attempted to persevere at the 2016 European Athletics Championships, but dropped out of the heats and brought his season to a close. His injury rehabilitation in the 2017 season was slow, and he continued to experience pain while running, while affected his performances that year. Competing with the British 4 × 100 metres relay quartet, the team failed to finish at the 2017 IAAF World Relays, but set a championship record of 38.08 seconds to win at the 2017 European Team Championships. Hughes placed fourth in the 200 m at the Adidas Boost Boston Games and 2017 British Athletics Championships. On the 2017 IAAF Diamond League circuit he was fifth at the London Grand Prix then had a season's best of 20.22 seconds for third at the Rabat Meeting. His injuries left him drained in the rounds at the 2017 World Championships in Athletics and he ended up seventh in his semi-final. His performances improved towards the end of the year, with third place in the 100 m at the British Athletics Grand Prix in Birmingham and sixth at the Memorial Van Damme 200 m.