Classifying organisms has a wide use and a long history in ecology. However, the meaning of a ‘group of organisms’ and how to group organisms is still the subject of much theoretical and empirical work. Achieving this long quest requires simplifying the complexity of species niches for which relevant morphological, behavioural, biochemical or life-history traits are often used as relevant proxies. Soil fauna is highly diverse and many classifications have been proposed to synthesize both the response of soil organisms to their environment and their effect on soil functioning. Here, we provide a critical overview of the characteristics and limitations of the existing classifications in soil ecology, and propose clarifications and alternatives to current practices. We summarise the similarities and differences in how classifications have been created and used in soil ecology. We propose a harmonization of the current concepts by properly defining ‘guilds’, ‘functional groups’ and ‘trophic groups’ as subcategories of ‘ecological groups’, with different purposes and distinguishing criteria. Finally, based on these concepts, we suggest a common framework to define classifications based on functional traits that allows a better and unified understanding of changes in soil biodiversity and ecosystem functioning.