Composting involves diverse communities of microorganisms, both unicellular and multicellular, which play their role at different stages of the process. The constant change in the microenvironment provides selective advantage to those organisms that can survive best at a given time.

Bacteria make up 80–90% of the billions of microorganisms found in a gram of compost. At the highest compost temperature, bacteria of the genus Thermus are isolated, indicating their dominance during the thermophilic phase of composting.

Actinomycetes are filamentous type of bacteria that also play a role in the composting process. As composting proceeds, temperature changes correspond to the dominance of specific communities of microorganisms at work.

Protozoans are single-celled microscopic organisms found in water droplets trapped in the compost matrix. Their role in composting is that of a secondary consumer as they sustain on organic material, bacteria, and fungi.

In addition to microorganisms, compost contains a large variety of insects, mites, snow bugs, ants, earthworms and other worms. Vermiculture is part of composting, and the presence of worms indicates soil fertility. Composting represents a natural way of regenerating soil fertility.