Strong acid digestions are commonly used to determine heavy metal (HM) contents in soils. In order to understand more fully the acid digestion processes, a logical step is to determine the extent of dissolution of mineral phases. The aims of this study were to compare the efficiency of extraction of HM by different acid digestions and to monitor the associated dissolution of the clay fraction. The context of the study was to develop a milder chemical extraction method (microwave-assisted 1 mol L−1 HNO3 closed system (NACS)), which recovers more reactive HM and with little dissolution of minerals. The different acid digestion methods dissolved different amounts of minerals from the clay fraction. Both aqua regia (AR) and EPA 3051 dissolved all of the Fe and Al oxides, and the dissolution of kaolin was limited to thinner particles (c dimension), smaller particles in a and b dimensions and grains with lower crystallinity. The lower recovery of HM for AR compared with EPA 3051 was related to the large amount of short-range order phases formed during the AR extraction as these phases have the capacity to re-adsorb HM. The new method (NACS) has the potential to replace other methods of determining bioavailable forms of HM, such as AR and EPA 3051. The contents of Pb, As, Co, Zn, and Cu determined by EPA 3051 and EPA 3052 were quite close.