The purpose of this work is to investigate a new class of solvents for separating secondary agricultural residues, which have already been transported to processing centers, into individual biomass components. Using biocompatible deep eutectic solvents (DES) on secondary agricultural residues could valorize these wastes into bioproducts by separating lignin from cellulose. DES pretreatment to achieve this separation involves chemicals that are less hazardous for the environment than other pretreatments. Methods Five deep eutectic solvents that are biocompatible have been investigated for their ability to deconstruct rice hulls and sugarcane bagasse. Mass yield, enzymatic hydrolysis of the pretreated biomass, fiber analysis, pKa analysis and Fourier transform infrared spectroscopy (FTIR) were performed to explore the effect of the DES on these secondary agricultural residues. Results Experimental results confirmed that the DES formic acid:choline chloride (FA:CC), lactic acid:choline chloride, and acetic acid:choline chloride were effective in removing lignin, thus concentrating cellulose in both pretreated biomass. Addition of water precipitated lignin from the spent DES, as confirmed by FTIR. However, the higher pKa DES lactic acid:betaine and lactic acid:proline had little effect on rice hulls or sugarcane bagasse. FA:CC was the most effective of the DES tested in preparing the biomass for enzymatic saccharification. All the effectively pretreated samples had higher inorganic content compared to the relevant raw biomass. Conclusions DES with stronger acidity (lower pKa) were found to be more efficient for delignification, leading to higher glucose yield. Further work is required to determine how inorganics affect waste biomass pretreatment.