Soil biodiversity provides both direct (the organisms themselves and/or their metabolic products) and indirect (the long-term outcome of their activities) services to mankind. Therefore, the term 'ecosystem service' was coined (Gómez-Baggethun et al. 2010), so as to be able to put an economic value on biodiversity in general and soil biodiversity in particular. Selected organisms from different functional groups (i.e.microsymbionts, decomposers, elemental transformers, soil ecosystem engineers, soil-borne pest and diseases, and microregulators) are used to illustrate the linkages of soil biota and ecosystem services essential to life on earth as well as with those associated with the provision of goods and the regulation of ecosystem processes. These services are not only essential to ecosystem function but also a critical resource for the sustainable management of agricultural ecosystems (Barrios, 2007). Values have been established for particular soil functions. (Download table of economic value).

Species diversity of soil organisms maintains the functions and resilience of soil. Any perturbation may affect soil activity and any deleterious outside effects can be reduced if the functions of the soil are spread amongst different species. Removal of one keystone species or ecosystem engineer, may lead to catastrophic effects on the ecosystem. Similarly, the introduction of a keystone organism may also have catastrophic or beneficial effects, depending on the situation (Barros, 1999). This can be considered to be 'ecological health' and results from the many components which make up functions such as nutrient cycling or energy transfers. Soil biodiversity and soil health can also be seen as one measure of environmental quality, because the functioning of the soil system may be the key to understanding the health of agroecosystems.

Regardless of any ecological or monetary value, several authors (Hågvar, 1994; McNeely et al., 1995) have mentioned ethical and moral reasons why biodiversity should be conserved.  Most of the world’s religions give intrinsic worth to the natural world, and it is unlikely that this deep-seated notion will disappear, even despite the force of the economic values placed on biodiversity. However, the world view that denies any sacred value or self-worth to nature is being rapidly spread throughout the world by globalization and modern industrial societies who view the world as a warehouse of commodities for human enjoyment. The danger of this to biodiversity conservation should not be underestimated, although the possibility of using biodiversity for enjoyment (e.g. ecotourism) and other benefits may serve to counteract the negative forces of ecologically ignorant consumer societies.