Iran is the highest producer of pistachio worldwide and has an annual production of about ???,??? tons of fresh pistachio by-product. Due to its high organic and phenolic content as well as high solids concentration, pistachio processing wastes create significant waste management problems unless they are properly managed. Anaerobic digestion is one of the acceptable environmental and economic technologies to control the pistachio wastes and produce energy and enrich fertilizer for soil. Good digestion for different wastes needs suitable mixture for co-substrates and pretreatments. Therefore, effect of different mixture of pistachio waste: cow manure and pretreatment factors of NaOH and H?O? was studied in this research. Co-digestion was done in the ??? mL digesters for mesophilic condition using a combined D-optimal design. Their CH? production were measured for ?? days. Then a model was developed among the CH? production and amounts of pistachio waste, cow manure, NaOH and H?O? to determine the effects of these parameters on the CH? production. Model P-value was lower than ?.???? and its lack of fit was ?.??, predicted R? was ?.?? in reasonable agreement with adjusted R? of ?.??. Adequate precision was ?.? indicated an adequate signal for the model. Further, standard error of the model equaled to ?.? which was very low, model R? equaled to ?.?? and adjusted R? was ?.?? which were high, indicating that the model was suitable for CH? estimation. By illustrating the model in ?D graphs, it was shown that the use of NaOH had negative effect on the CH? production while H?O? had positive effect on the CH? production. Higher amounts of cow manure improved the CH? production while higher amounts of pistachio wastes decreased the CH? production. These may happen because of the high amounts of phenolic and antioxidant compounds in the pistachio waste which are harmful for anaerobic microbes