Enhancement of biogas and biohydrogen production from cotton plant wastes (stalk and boll) was investigated in the current work. This was achieved using alkaline pretreatment by sodium hydroxide solution of 8% (w/w) concentration at 0 and 100 degrees C for 10, 30, and 60 min, together with ammonia solution of 4 and 8% (w/w) concentrations at 40 and 80 degrees C for 6 and 12 h. Maximum biogas production values of 246 and 219 mL/g volatile solids (VS) were achieved respectively from boll pretreated by sodium hydroxide 8% (w/w) at 100 C for 10 min and stalk pretreated by ammonia solution 4% (w/w) at 80 degrees C for 12 h. Sodium hydroxide-pretreated boll and ammonia solution-pretreated stalk, under conditions similar to those leading to the maximum methane production, gave maximal hydrogen production values of 17 and 15.2 mL/g VS, respectively. The results of hydrogen production in this study showed satisfactory agreement with the Gompertz equation. Structural analysis of the samples using scanning electron microscopy and Fourier transform infrared spectroscopy established that the reduction of crystallinity, lignin removal, and increase in porosity of the pretreated samples were the main reasons behind these observations.