The effects of ammonia on semicontinuous anaerobic digestion (AD) of food waste were studied. Inhibition effects were observed when the total ammonium concentration in the AD reactor exceeded 2g/L. Ammonia strongly inhibited methanogenesis but minimally affected hydrolysis and acidification. Inhibition of AD by ammonia enhanced the accumulation of acetate and propionate and consequently decreased the pH, which worsened the inhibition effects. With increasing ammonium concentration, methane production from acetate shifted from acetoclastic methanogenesis (mostly by Methanosaeta) to syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis (mostly by Methanosarcina). The metabolism of hydrogenotrophic methanogens Methanobacterium and Methanospirillum were inhibited when the ammonium concentration further increased to about 6 g/L. Microorganisms irrelevant in the methane fermentation process were enriched with the increase of ammonium concentration.