Soils are impacted globally by several anthropogenic factors, including chemical pollutants. Among those, perfluoroalkyl and polyfluoroalkyl substances (PFAS) are of concern due to their high environmental persistence, and as they might affect soil structure and function. However, data on impacts of PFAS on soil structure and microbially-driven processes are currently lacking. This study explored the effects of perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorobutanesulfonic acid (PFBS) at environmental-relevant concentrations on soil health, using a 6-week microcosm experiment. PFAS (even at 0.5 ng g−1 for PFBS) significantly increased litter decomposition, associated with positive effects on β-glucosidase activities. This effect increased with PFAS concentrations. Soil pH was significantly increased, likely as a direct consequence of increased litter decomposition affected by PFAS. Soil respiration was significantly inhibited by PFAS in week 3, while this effect was more variable in week 6. Water-stable aggregates were negatively affected by PFOS, possibly related to microbial shifts. PFAS affected soil bacterial and fungal abundance, but not microbial and certain enzyme activities. Our work highlights the potential effects of PFAS on soil health, and we argue that this substance class could be a factor of environmental change of potentially broad relevance in terrestrial ecosystem functioning.