Soil pollution with heavy metals is a worldwide environmental problem. Phytoremediation through phytoextraction and phytostabilization appears to be a promising technology for the remediation of polluted soils. It is important to strongly emphasize that the ultimate goal of a heavy metal remediation process must be not only to remove the heavy metals from the soil (or instead to reduce their bioavailability and mobility) but also to restore soil quality. Soil quality is defined as the capacity of a given soil to perform its functions. Soil microbial properties are increasingly being used as biological indicators of soil quality due to their quick response, high sensitivity, and, above all, capacity to provide information that integrates many environmental factors. Indeed, microbial properties are among the most ecologically relevant indicators of soil quality. Consequently, microbial monitoring of the recovery of soil quality is often carried out during heavy metal phytoremediation processes. However, soil microbial properties are highly context dependent and difficult to interpret. For a better interpretation of microbial properties as indicators of soil quality, they may be grouped within categories of higher ecological relevance, such as soil functions, ecosystem health attributes, and ecosystem services.