Per- and polyfluoroalkyl substances (PFAS) have emerged as significant environmental contaminants due to their persistence, bioaccumulative properties, and potential adverse impacts on health and ecosystems. Water Resource Recovery Facilities (WRRFs) play a crucial role in the management of PFAS, given their widespread presence in consumer products and subsequent reintroduction into the environment. This study investigated the dynamics of PFAS within the solids stream treatment processing that utilized autothermal thermophilic aerobic digestion (ATAD) followed by a storage nitrification-denitrification reactor (SNDR). PFAS analysis included 60 PFAS analyzed via liquid chromatography-triple quadrupole time-of-flight mass spectrometry of pre-ATAD, post-ATAD, and post-SNDR samples. Complexities such as volatile solids loss during the treatment processes were considered in assessing the effect of ATAD and SNDR on PFAS concentrations. Significant changes were observed in the relative contributions of various PFAS classes throughout the treatment processes due to biotransformation; similar changes were reflected in both 2019 and 2021. The relative contribution of perfluoroalkyl alkyl acids (PFAAs) increased while phosphorus-containing PFAS (e.g., di-substituted polyfluoroalkyl phosphate esters) and fluorotelomer carboxylic acids decreased. Shorter-chain PFAAs were enriched during ATAD, whereas most PFAS increased during SNDR except diPAPs and FTCAs, reflecting treatment conditions' impact. Overall, minor decreases in total PFAS concentrations during ATAD as well as SNDR were observed and hypothesized to be due to enhanced biotransformation to ultra-short PFAS that were not quantified. Even with up to 60 PFAS quantified in the samples, PFAS accounted for <1% of the total fluorine with <2% of that total fluorine being fluoride prompting interest in additional exploration.