Microbial communities regulate the transformation and stabilization of nutrients during composting; however, current knowledge on their specific functional roles across composting stages remains poorly integrated. This review examines the pivotal role of microbial mediation in nitrogen (N) and phosphorus (P) dynamics during composting and their subsequent impact on soil health. We analyze how biotechnological interventions—specifically the inoculation of functional microbial consortia (phosphate-solubilizing bacteria, phosphate-accumulating bacteria, and nitrifiers) and the application of physicochemical additives such as biochar—reconfigure microbial succession patterns to mitigate gaseous losses and enhance nutrient bioavailability. Several studies have reported substantial reductions in ammonia (NH₃) and nitrous oxide (N₂O) emissions under specific composting conditions, while simultaneously promoting the stabilization of labile P into more recalcitrant forms, including polyphosphates. Furthermore, the application of mature compost to agricultural systems induces a profound ecological reassembly of the soil microbiome, shifting community composition toward copiotrophic dominance (Pseudomonadota and Bacteroidota) and increasing functional redundancy. These microbial and functional shifts enhance soil resilience to environmental stressors—such as drought and temperature fluctuations—by stabilizing extracellular enzyme activity and reinforcing microbial co-occurrence networks. We conclude that managing microbial interactions along the compost–soil continuum is essential for developing organic amendments optimized for specific soil and crop requirements. This integrated approach represents a cornerstone of precision sustainable agriculture and contributes to climate change mitigation through soil health restoration.