Flexible flatfoot in childhood usually undergoes a spontaneous return to normal. However, during this process, it remains unclear whether the gait pattern will be adjusted concurrently and the mechanism of such adjustment. We investigated the mechanism underlying the change in gait patterns in children after the natural recovery of flat feet through a two-year follow-up study, from the perspectives of plantar loading and gait stability. A total of 15 flatfoot children in the recovery group and 17 typically developed children in the control group were included after extensive sample screening. Three data acquisitions of plantar pressure and Center Of Pressure (COP) were performed every 12 months using a Footscan® pressure plate. Independent t-tests and statistical parametric mapping analysis were used to explore differences between the recovery and control groups at each measurement. At baseline, the recovery group showed higher midfoot loading and a more laterally shifted COP. At the 12-month point, the recovery group manifested a significantly lower load ratio but higher standardized maximum force at the lateral forefoot. At the 24-month point, the recovery group changed to show a considerably higher load ratio under the second metatarsal head, accompanied by a more lateral and posterior COP displacement at the late stance phase. During the recovery of flexible flatfoot morphology in childhood, gait patterns eventually show significant improvement while exhibiting different characteristics at various stages. This study reveals the biomechanical adaptations following the natural recovery of flatfoot in children, contributing to a comprehensive understanding of the impact of pediatric flatfoot.