Organisms play a central role in how soil is formed and are involved from the initial 'biological weathering' of parent material to the turnover and incorporation of organic material into the soil. Weathering of the parent material is the main source of minerals which enter into the ecosystem. The organic matter which builds up in soil over time is related to the diversity of the organisms which colonise the parent material and the conditions under which the soil is forming.

The bedrock or parent material is first weathered through physical processes such as frost action and later through indirect biological activity from the production of organic acids by primary colonising organisms such as lichens and other carbon-fixing autotrophs. Eventually, organic material builds up which supplies carbon to other organisms and can eventually support the growth of larger plants. When sufficient soil has accumulated, soil animals, such as mites and earthworms mix the soil further and aid in distributing soil microorganisms.

Microorganisms can play a more direct role in soil formation. The action of bacteria and fungi on soil minerals such as feldspar, a component of granitic rock, release valuable elements such as potassium into the ecosystem. On the other hand, fungi such as Penicillium have been shown to precipitate soil minerals such a hydromagnesite thereby promoting mineral neoformation.