Single-stage (S-N treatment) and two-stage anaerobic digestion with (T-R treatment) and without digestate recirculation (T-N treatment) for methane production using food waste (FW) were comparatively evaluated to examine the effects of digestate recirculation on anaerobic digestion (AD). Digestate recirculation positively affected the methane yield and organic loading rate (OLR). Metabolite correlation analysis revealed that a systematic hydrolysis degree of greater than 75% is crucial to achieve the complete recoverable yield of methane from FW. Digestate recirculation also markedly increased the system alkalinity, maintaining an optimum pH for methanogens. However, the ammonium accumulated by T-R treatment would destroy the metabolic balance between the hydrolytic bacteria and methanogens, especially at a critical OLR. Therefore, the appropriate control of two-stage AD systems with digestate recirculation is limited not only to OLR regulation but also to the prevention of ammonium accumulation.