Soil quality is threatened by the increase in human population and by the fact that most of the cultivable land is intensively used. The initial interest in this topic focused on defining soil quality but shifted into how to measure soil quality in the late 1990s. There is a general agreement that soil biochemical, microbiological and biological properties are more suitable than physical and/or chemical properties for the purpose of estimating alterations in soil quality and hence soil degradation. To date, most studies have used microbial biomass, soil respiration and enzymatic activities to obtain soil quality indices, whereas less focus has been given to soil fauna (microarthropods and nematodes). This article aims to do a critical review of soil quality indices based on soil biological and biochemical activities, mainly microbial biomass, soil respiration and the activity of several enzymes. Limitations within the database of articles that are focussed on broad scale application of soil quality indices include the difficulty of selecting the highest quality soils for comparison purposes, lack of standardisation of analytical methods, and inclusion of an insufficient number of soil types and ecosystems. There is a need to validate soil quality indices, both, spatially and temporally and to explore the use of indices that integrate faunal and microbial measurements. Copyright © 2013 John Wiley & Sons, Ltd.