Per- and polyfluoroalkyl substances (PFAS) are recalcitrant pollutants which tend to persist in soils and aquatic environments and their remediation is among the most challenging with respect to organic pollutants. Anaerobic digestion (AD) supplemented with low amounts of carbon materials (CM), acting as electron drivers, has proved to be an efficient process for the removal of organic compounds from wastewater. This work explores the impact of PFAS on different trophic groups in anaerobic communities, and the effect of carbon nanotubes (CNT), activated carbon (AC), and oxidized AC (AC-HNO3), as electron shuttles on the anaerobic bioremoval of these compounds, based on CH4 production. The inhibition of the specific methanogenic activity (SMA) exerted by perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), at a concentration of 0.1 mg L−1, was below 10% for acetoclastic and below 15%, for acetogenic communities. Hydrogenotrophic methanogens were not affected by the presence of PFAS. All CM reduced the negative impact of PFAS on the CH4 production rate, but AC was the best. Moreover, the methanization percentage (MP) of sewage sludge (SS) increased 41% in the presence of PFOS (1.2 g L−1) and AC. In addition, AC fostered an increase of 11% in the MP of SS+PFOS, relative to the condition without AC. AC promoted detoxification of PFOA- and PFOS-treated samples by 51% and 35%, respectively, as assessed by Vibrio fischeri assays, demonstrating the advantage of bringing AD and CM together for PFAS remediation.