Anaerobic digestion for the valorization of organic wastes into biogas is gaining worldwide interest. Nonetheless, the sizing of the biogas plant units require knowledge of the quantity of feedstock, and their associated methane potentials, estimated widely by Biochemical Methane Potential (BMP) tests. Discrepancies exist among laboratories due to variability of protocols adopted and operational factors used. The aim of this study is to verify the influence of some operational factors (e.g., analysis frequency, trace elements and vitamins solution addition and flushing gas), feedstock conservation and the source of inoculum on BMP. Among the operational parameters tested on cellulose degradation, only the type of gas used for flushing headspace of BMP assays had shown a significant influence on methane yields from cellulose. Methane yields of 344 ± 6 NL CH4 kg−1 VS and 321 ± 10 NL CH4 kg−1 VS obtained from assays flushed with pure N2 and N2/CO2 (60/40 v/v). The origin of inoculum (fed in co-digestion) only significantly affected the methane yields for straw, 253 ± 3 and 333 ± 3 NL CH4 kg−1 VS. Finally, freezing/thawing cycle effect depended of the substrate (tested on biowaste, manure, straw and WWTP sludge) with a possible effect of water content substrate.