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The widespread use of perfluoroalkylated acids (PFAAs) has led to a global presence in the environment, in which they accumulate and may cause detrimental effects. Although soils are known sinks for many persistent organic pollutants, still little is known on the behaviour of PFAAs in soils. Furthermore, studies that examine the relationships between PFAA concentrations and soil microbial parameters are scarce. The 3 M fluorochemical plant near Antwerp has been characterized as a PFAAs hotspot. In the present study, we examined the vertical distribution of 15 PFAAs and their associations with multiple physicochemical soil properties along a distance gradient from this hotspot. Additionally, we tested the relationships between PFAA concentrations in the top soil with soil respiration, microbial activity and microbial biomass. Our results show that both perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) concentrations were elevated in the subsurface layer (up to 50 cm), after which concentrations decreased again, suggesting a downward migration of both analytes in the soil. This downward movement might pose a potential threat for the contamination of the groundwater and, consequently, organisms that rely on this water for consumption. The soil concentrations were influenced by multiple physicochemical properties of the soil, which suggests differences in bioavailability and sorption/desorption capacities between different soil types. We did not observe any influence of PFAA contamination in the top soil on microbial activity and biomass nor soil respiration.