An anaerobic membrane bioreactor (AnMBR) pilot plant treating kitchen food waste (FW) jointly with urban wastewater was run for 536 days. Different operational conditions were tested varying the sludge retention time (SRT), the hydraulic retention time (HRT) and the penetration factor (PF) of food waste disposers. COD removal efficiency exceeded 90% in all tested conditions. The joint treatment resulted in an almost 3-fold increase in methane production (at 70 days of SRT, 24 h HRT and 80% PF) in comparison with the treatment of urban wastewater only. Mathematical model simulations and Illumina technology were used to obtain in-depth information of this outstanding process performance. Both the PF and SRT factors increased influent biodegradability. The experimental results were accurately reproduced via model simulations modifying only the influent biodegradability. The high SRT and the presence of ground FW in the influent resulted in higher hydrolytic activity. Not only did the Archaea population increase 3-fold but Levilinea genera was also significantly raised. Three new genera characterised by anaerobic fermentation of amino acids (Leptolinea, Aminomonas and Aminobacterium) were among the ten most abundant of the total sequences identified during the joint treatment, indicating an improvement in the hydrolysis step of anaerobic degradation. Influent biodegradability remained at high values when FW addition stopped.