There is significant interest in the treatment of swine manure, which is a hazardous biowaste and a source of pathogenic contamination. This work investigated the effects of microorganism-mediated inoculants (MMIs) on nutrient flows related to humification or phosphorus (P) dynamics during the aerobic composting of swine manure. The impact of MMIs on microbe succession was also evaluated. The addition of MMIs had positive effects associated with nutrient flows, including thermal activation, decreases in certain fluorescence emissions, lower mass loss and variations in levels of certain elements and functional groups. MMIs altered the maturation behavior and kinetics of organic matter while improving microbial activity. Phosphorus was found in the compost in the forms of MgNH4PO4·6H2O crystals and Poly-P as the IP species, and Mono-P as the OP species in compost generated from the dissolution or inter-transformation among P pools. These nutrient flows are attributed to changes in the structure of microbial communities as a consequence of introducing MMIs. Diverse microbial compositions were identified in different composting phases, although Bacillus appeared in each phase. This work provides support for the aerobic composting of hazardous biowaste as well as an improved understanding of nutrient flows, as a means of producing higher quality compost.