Scientific theory largely neglects linkage between organic phosphorus (Po) mineralization rate and dispersal potential of alkaline phosphatase-encoding bacteria (PEB) containing the phoD gene. Different densities of substrates (i.e., compacted soils, culture media, and soil aggregates) were prepared and molecular tools were used to unveil relationship between dispersal potential of PEB and Po mineralization rate. According to morphological observations and ecological studies, we found that the stronger dispersal potential of PEB ensured a higher Po mineralization rate. Higher Po mineralization rates were found in soil microaggregates than in macroaggregates and silt + clay, and soil Po mineralization rate was related closely to P fractions distributed heterogeneously in aggregates. The phoD gene abundance was notably correlated with Po mineralization rate, and rare PEB mediated Po mineralization. The Bradyrhizobium as identified genus dominated in dramatically heterogeneous PEB community, and stochasticity (70.5–89.5%) affected more on community assemblages of PEB. The PEB showed a stronger dispersal potential in microaggregates than the other aggregates, as indicated by weaker community stability, stronger species replacement, higher migration rate, lower environmental constraint, and broader niche breadth. Overall, our results emphasize that a stronger dispersal potential of PEB ensure a higher Po mineralization rate, and these findings broaden our understanding of how PEB maintain landscape and function in soils.