Characterisation of the fouling attached to PVDF membranes treating an anaerobic effluent for dissolved CH4 recovery was carried out. A commercial flat-sheet PVDF membrane and a PVDF functionalised by grafting of organofluorosilanes (mPVDF) that increased its hydrophobicity were subjected to a continuous flux of an anaerobic reactor effluent in long-term operation tests (> 800 h). The fouling cakes were studied by the membrane autopsy after these tests, combining a staining technique, FTIR, and FESEM-EDX, and the fouling extraction with water and NaOH solutions. Both organic and inorganic fouling were observed, and the main foulants were proteins, polysaccharides, and different calcium and phosphate salts. Also, a significant amount of live cells was detected on the fouling cake (especially on the non-modified PVDF). Although the fouling cake composition was quite heterogeneous, a stratification was observed, with the inorganic fouling mainly in the bulk centre of the cake and the organic fouling mainly located in the lower and upper surfaces of the cake. The mPVDF suffered a more severe fouling, likely owing to a stronger hydrophobic-hydrophobic interaction with the foulants. Irreversible fouling remained on both membranes after the extraction, although a higher irreversible fouling was detected in the mPVDF; however, a complete polysaccharide removal was observed. Regarding the operation performance, PVDF showed a lower stability and suffered a severe degradation, resulting in a lower thickness and perforations. Finally, the decrease in the methane recovery performance of both membranes was associated with the fouling depositions.