Composting is a biologically driven process in which microbial communities mediate the transformation of organic waste into stable, nutrient-rich amendments. Accurate characterisation of these communities and their metabolic functions is critical for optimising compost quality, understanding nutrient cycling, and minimising environmental impacts. This chapter provides a comprehensive overview of the methodological advancements used to investigate microbial community structure and functional dynamics in composting systems. Traditional culture-based techniques have limited resolution, capturing only a small fraction of microbial diversity. In contrast, high-throughput molecular approaches—such as metagenomics, metatranscriptomics, and metaproteomics—enable in-depth taxonomic profiling and functional annotation of microbial communities, including unculturable taxa. These omics-based methods allow for the identification of genes, transcripts, and proteins associated with key processes such as organic matter degradation, nitrogen transformation, and antibiotic resistance dissemination. Polymerase chain reaction (PCR)-based methods, particularly quantitative PCR (qPCR) and digital PCR (dPCR), offer high sensitivity in quantifying specific microbial genes related to metabolic pathways. dPCR, in particular, provides absolute quantification without reliance on standard curves, improving reproducibility across studies. Stable isotope probing (SIP), when combined with nucleic acid or protein analyses, offers direct evidence of microbial assimilation of labelled substrates, thereby linking taxonomic identity to metabolic function. Despite significant progress, challenges remain, including biases in amplification-based methods, limited reference databases for functional annotation, and high costs associated with omics and SIP techniques. Nevertheless, the integration of complementary approaches enhances the resolution of microbial and metabolic dynamics across composting phases. Overall, the application of multi-omics and targeted molecular tools has substantially advanced the understanding of microbial ecology in composting environments. These methods provide a foundation for the development of strategies to improve composting efficiency, assess environmental risks, and inform sustainable waste management and soil fertility practices.