Following the Olympics, Manaudou competed at the 2012 European Short Course Championships and the 2012 World Short Course Championships held at the end of 2012. At the European Championships in Chartres, Manaudou won five gold medals including an individual title in the 50-meter freestyle with a time of 20.70. At the World Short Course Championships in Istanbul, Manaudou won one silver and bronze medal. In his specialty event, the 50-meter freestyle, Manaudou placed second behind Russian swimmer Vladimir Morozov (who he beat in Chartres) by three tenths of a second (0.33) with a time of 20.88.