A semicontinuous test of the biomethane potential of primary sludge (PS), cheese whey (CW) and cow manure (CM) has been investigated with automatic methane potential system (AMPTS II) for 68 days (38 °C). Four different combinations of substrates were used at different organic loadings and hydraulic retention times. During the test, we performed measurements of physico-chemical parameters (pH, electrical conductivity, SFACs, COD, microelements, dry matter, alkalinity) and optimized the process with univariate and multivariate statistical analysis. After 50-days of stable methane production, we doubled cheese whey concentrations. According to all analytical methods, stable methane production was observed in all combinations of substrates. The methane yield was correlated with the amount of cheese whey addition. According to our observations, cheese whey was the main source of SCFAs in the system, while cow manure contributed to the stability of the process with increasing buffer capacity. We detected higher concentrations of SCFAs in the process without cow manure addition. pH, alkalinity and SCFAs were the most important parameters according to nonmetric multidimensional scaling analysis. We observed potential problems in process stability in the extension of the process, because of decreasing concentrations of some microelements, because of washing out of the reactors. The highest methane yields in the first 50 days were observed at a PS:CW:CM ratio of 70:55:10. The most stable process after doubling CW addition was observed at a ratio of 70:70:10.