Soil biota (soil microflora, soil animals) are sensitive to soil pH, either directly upon contact or after soil ingestion or indirectly through the various soil properties to which pH contributes (e.g. nutrient status, metal toxicity, humus form). According to the various physiological and behavioural adaptations of soil biota, the species composition of soil microbial and animal communities varies with soil pH. Along altitudinal gradients, changes in the species distribution of soil animal and microbial communities can be at least partly ascribed to variation in soil pH. The shift from toxic to non-toxic forms of aluminium around pH5 marks the passage from acid-tolerance to acid-intolerance, with few changes in the species composition of soil communities above this threshold, even in calcareous soils. Soil animals exhibit distinct pH preferences when allowed to exert a choice along a range of pH values, explaining that various field distributions of soil organisms, motile microbes included, could at least partly result from active movement along pH gradients. Like for plants, competition between acido-tolerant and acido-intolerant soil-dwelling organisms was suspected to play a role in the shifts in species composition observed along pH ranges.
The opposition between acido-tolerance and acido-intolerance is commonly observed at species level within a genus or at genus level within a family, but it also occurs at much higher taxonomic rank, like between soil fungi and bacteria, here too with a strong involvement of competition.
It has been suggested that soil organisms more tolerant of soil acidity, and thus living mainly in soils at pH less than 5, were more primitive than those intolerant of soil acidity. A cladistic analysis on the collembolan genus Willemia showed that tolerance to soil acidity was correlated with tolerance of other stress factors and that stress tolerance was an ancestral character in this genus. However the generality of these findings remains to be established.
At low pH,  the oxidative stress induced by aluminium (Al) affects soil animals the body of which is not protected by a thick chitinous exoskeleton like in arthropods, and thus are in more direct contact with the soil solution, e.g. protists, nematodes, rotifers (microfauna), enchytraeids (mesofauna) and earthworms (macrofauna).
Effects of pH on soil biota can be mediated by the various functional interactions of soil foodwebs. It has been shown experimentally that the collembolan Heteromurus nitidus, commonly living in soils at pH higher than 5, could be cultured in more acid soils provided that predators were absent. Its attraction to earthworm excreta (mucus, urine, faeces), mediated by ammonia emission, provides food and shelter within earthworm burrows in mull humus forms associated with less acid soils.