In this study 26 new oligophenol cellulase inhibitors were discovered from wheat straw pretreatment liquors. By consideration of the reaction mechanisms for their formation it is proposed that these oligophenols are formed during hydrothermal biomass pretreatment by pentose self-condensation reactions involving aldol condensations, 1,4 additions to α,β unsaturated carbonyl compounds, 3-keto acid decarboxylations and oxidations. Furthermore, pentose reactions with phenolic lignin components are suggested. The identification of the central role of xylose in the reaction routes for oligophenolic inhibitor formation led to the solution to protect the reactive anomeric center in xylose. It is shown that protection of the anomeric center in in situ generated xylose with ethylene glycol monobutyl ether, during pretreatment of wheat straw, reduces the level of oligophenols by 73%. The results pave the way for implementation of new types of reactions that hinder inhibitor formation in lignocellulosic biomass processing.