This study aimed to evaluate the possibility of acidogenic phase as the pretreatment method of filter cake (FC) before being co-digested with biogas effluent (BE), and anaerobic sludge (AS) for methane production. The effects of separation of acidogenic and methanogenic phases on the improvement of the methane production process from a co-digestion of FC with BE, and AS were also investigated. FC was pretreated through acidogenic phase anaerobic digestion (AD) using a different substrate to inoculum ratios (SIRs) and substrate concentrations. The optimum conditions for acidogenic phase AD of FC were SIRs of 4:1 and substrate concentration of 15.0\% total solid (TS). Resultantly, the maximum volatile fatty acids (VFA) yield of 0.17 g-VFAs/g-VS (volatile solids) was obtained. The major VFA components were butyric and acetic acid. The acidogenic phase of FC was semi-continuously conducted in a continuous stirred tank reactor (CSTR) at various hydraulic retention time (HRT). The highest concentration and yield of VFAs of 7.29 g/L and 0.39 g-VFAs/g-VS, respectively, were observed at HRT of 5 d. The major VFAs observed were butyric acid (48.8\%), and acetic acid (36.8\%). Subsequently, the proportions of pretreated FC, BE, and AS to produce methane were optimized in batch experiments. The highest methane yield (MY) of 195.9 mL-CH4/g-VS was achieved at the proportions of pretreated FC and BE of 37.75 and 22.25 g-VS/L, respectively, without the addition of AS. The optimum substrate proportion was further used to determine the MY in a 10 L CSTR with the various HRT. The maximum MY of 130.5 mL-CH4/g-VS was achieved at an HRT of 20 d which produced an EY of 4.7 kJ/g-VS. Analysis of microbial community by 16S rRNA amplicon sequencing on an illumination platform indicated that genera Rummeliibacillus, Lactobacillus, and Bacillus were the dominant bacteria found in the acidogenic phase. Methanoculleus and Methanosarcina were found to be the most dominant genera in methane fermentation. Results suggested that acidogenic phase digestion can be used as an alternative method for FC pretreatment to improve methane production. Furthermore, the separation of acidogenic and methanogenic phases improves the process stability.