This study focuses on thermal and non-thermal effects of microwave pretreatment on horse dung as indigenous inoculum before xylose and wheat straw fermentation, emphasizing metabolite production and microbial community changes. Two horse dung microwave pretreatments (MW40°C and MW95°C) were compared with a conventional thermal pretreatment (Th95°C) and an unpretreated condition (Ctrl). Microwave heating pretreatment (MW95°C) leads to similar production as a conventional thermal pretreatment (Th95°C) for xylose and wheat straw fermentation while MW40°C treatment was similar to the control. The two thermal pretreatments (MW95°C and Th95°C) produced respectively 19 % and 45 % more than the Ctrl and MW40°C conditions. Nonetheless, for wheat straw, microwave irradiation without heating affected the microbial community by increasing the alpha diversity richness. The Ruminiclostridium genus, known for its hydrolytic activity, represented at least 25 % of the total relative abundance after fermentation with thermal shock pretreatment, potentially explaining the enhancement of the metabolite production from straw.