Discharge of food waste (FW) into sewer systems causes environmental issues, such as sewer blockage and odour problems. This study investigated the long-term effects of FW addition on sediment properties, microbial communities, and metabolic pathways using laboratory-scale reactors for 160-day incubation. The addition of 2 g/L FW increased the critical erosion shear stress of sediments by 40.63% and reduced their self-cleaning capacity by 39.46%. This was attributed to the fact that FW discharge increased extracellular polymeric substances (EPS) in sediments by 82.94%, especially aromatic protein with high hydrophobicity and high content of intermolecular hydrogen bonds, which was supported by the increased genes encoding aminoacyl-tRNA biosynthesis. The denser biofilm on the sediment surface hindered oxygen transfer to deeper sediment zones, and lowered oxidation-reduction potential below -400 mV. Microbial and metagenomic analysis revealed an enrichment of methanogenic archaea (e.g., Methanothrix) and sulfate-reducing bacteria (e.g., Desulforhabdus), along with increased genes for dissimilatory sulfate reduction and methanogenesis pathways of acetate and CO