In order to optimize the biogas recovery from the co-digestion of food waste (FW) and paper waste (PW), the effect of PW content on two-phase anaerobic digestion (TPAD) was investigated. The mixtures of FW and PW, with the ratios of 10:0, 8:2, 6:4 and 5:5 (total solids), were fed into TPAD to recover biomethane. After the long-term expriment, it is elucidated that the methanogenesis in TPAD was stable for PW ≤ 40%. When PW = 50%, NH4HCO3 was added to the methanogenic phase to provide nitrogen. As the indicators of the stability of the anaerobic process, the ammonia and alkalinity in the methanogenic phase were simulated for their decreasing trend. The simulation results quantified the nitrogen deficiency in the methanogenic phase for PW = 50%. Also, the comparison of alkalinity and ammonia revealed that ammonia was the major contributor to the alkalinity. Furthermore, via stoichiometric calculations, high C/N ratios were found to increase the microbial yield and exacerbated the nitrogen deficiency. In the energy estimation, adding PW showed significant increase only when PW ≥ 40%. It was concluded that 40% was the optimal PW content for bioenergy augmentation from co-digestion of FW and PW using TPAD.