Mineral binding is a major mechanism for soil carbon (C) stabilization, and mineral availability for C binding critically affects C storage. Yet, the mechanisms regulating mineral availability are poorly understood. Here, we showed that organic amendments in three long-term (23, 154, and 170 yrs, respectively) field experiments significantly increased mineral availability, particularly of short-range-ordered (SRO) phases. Two microcosm studies demonstrated that the presence of roots significantly increased mineral availability and promoted the formation of SRO phases. Mineral transformation experiments and isotopic labeling experiments provided direct evidence that citric acid, a major component of root exudates, promoted the formation of SRO minerals, and that SRO minerals acted as "nuclei" for C retention. Together, these findings indicate that soil organic amendments initialize a positive feedback loop by increasing mineral availability and promoting the formation of SRO minerals for further C binding, thereby possibly serving as a management tool for enhancing carbon storage in soils.