Microorganisms are the primary agents of decomposition. Particularly, fungi are considered the major contributors due to their ability to produce specific enzymes and the possibility to access new substrates through hyphae. In this review, we highlighted the role of fungi in decomposition and reconsider the role of bacteria, neglected in the past, identifying key research needs and knowledge. Particular attention is given to the succession of different taxa with different ecological role that are able to use a substrate that undergoes to chemical and structural modifications. The quality of substrates is a critical factor that influences the microbial community together with environmental variables, such as temperature and moisture. However, the microbial community is also able to influence the substrate characteristics.