We investigated the capability of microorganisms isolated from environments polluted with perfluoroalkyl acids (PFAAs) to conduct biotransformation of these emerging pollutants. Two different microbial consortia (chemoorganoheterotrophic bacteria and total yeast and molds) were isolated from two river sediments in Saitama and Osaka, Japan, known for long term pollution with perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA). The microbial consortia were incubated in the presence of added PFOS and PFOA, and decreases in concentrations of these compounds were between 46–69% and 16–36%, respectively. Decreases in concentrations were, in part, due to sorption on biomass, but defluorinated PFOS and PFOA products were not detected. However, untargeted analysis suggested the presence of several metabolites found only in samples from consortia with PFOS and PFOA but not in the control samples. Molecular formula candidates were narrowed down to two options, C18H28O5F and C21H27O4. It was assumed that these formulas were associated with unsaturated monofluorinated fatty acids and hydrocarbons with multiple unsaturated bonds or ring structures.