Per- and polyfluoroalkyl substances (PFASs) are frequently detected in aquatic environments. Longer chained perfluoroalkyl acids (PFAAs), in particular, have been found to bioaccumulate in a broad range of aquatic biota. PFAAs have a physiochemical similarity to naturally occurring fatty acids and could potentially disrupt metabolic processes, however, there has been limited study in this area, especially in aquatic species. In this study, the associations between PFAAs and metabolite profiles were investigated in crustaceans. Eastern School Prawn (Metapenaeus macleayi) were obtained from three different locations (n = 15 per location) with similar environmental conditions but different levels of PFAA contamination. The concentrations of PFAAs, fatty acids and amino acids were analysed and differences in PFAA and metabolite profiles were evaluated. Different PFAA profiles were mirrored by significant differences in the composition of both fatty acid and amino acid profiles, indicating a potential association between PFAA concentration and the composition of metabolites in prawns. These results highlight a need for further research investigating the impacts of PFAA exposure, with the current study providing a foundation for further investigation of the relationship between PFAA bioaccumulation and organism metabolism.