Aqueous film forming foams (AFFFs) containing perfluoroalkyl and polyfluoroalkyl substances (PFASs) are commonly deployed to extinguish hydrocarbon fuel fires, resulting in petroleum hydrocarbons coexisting with PFASs in contaminated soil. Nutrient-amended and aerated biopiles used for petroleum hydrocarbon bioremediation could cause unintended transformation of polyfluorinated substances into perfluoroalkyl carboxylates (PFCAs). The study sought to examine environmental behaviors of PFASs in engineered treatment facilities by monitoring AFFF-derived PFASs under three nutrient conditions. The influence of nutrient levels on degradation kinetics and efficiency was found to vary between the two chemical classes and among individual PFASs. A high number of compounds including the zwitterionic polyfluoroalkyl betaines that have aged in the field for two years were continuously biotransforming in lab reactors, demonstrating their slow kinetics and environmental persistence. The low yield to PFCAs implies that the processes such as the formation of bound residues or irreversible sorption might play a major role in reducing detectable levels of zwitterionic PFASs. The high persistence of betaines was further confirmed by the behaviors of a freshly spiked sulfonamide betaine. The study demonstrated complex chemical dynamics in AFFF-impacted soils and the challenges for predicting the fate of PFASs in soil biopiling facilities.