Foot-strike and the associated load rate are factors related to overuse injuries in runners. The purpose of this study was to analyse structural and functional changes in runners using floating heel running shoes, compared with runners using conventional footwear. A randomised control trial was conducted. Twenty runners with overuse injuries were followed over a 12-week gait retraining programme using floating heel running shoes or their conventional footwear. Pain was measured with pressure pain thresholds (PPTs), structural changes were measured with ultrasonography, and severity and impact of injury was scored on the Oslo Sports Trauma Research Centre Overuse Injury Questionnaire (OSTRC-O). Statistical differences were found between groups after the intervention (p < 0.001), with a medium size effect SE = 0.8, and the floating heel running shoes group reached higher PPTs values. Participants using floating heel running shoes showed higher OSTRC-O scores than those using their conventional footwear (p < 0.05), with higher scores after the intervention (p < 0.05). A 12-week gait retraining programme using floating heel running shoes had positive effects on the injury recovery process when compared to the use of conventional footwear, with significant differences in terms of pain and impact on sports activity.