The effectiveness of one-pot saccharification process combining pretreatment and enzymatic hydrolysis of biomass for fermentable sugar production is highly influenced by the choice of solvent media. The potential of choline-based ILs coupling with different anionic species remains underexplored regarding their compatibility with cellulase. Herein, the effects of choline-based ILs formulated with amino acids as anionic species on cellulase from Trichoderma reesei were evaluated using both experimental and computational approaches. Experimental results showed that endoglucanase I (EG I) exhibited no deactivation in choline glycinate ([Cho][Gly]), while cellobiohydrolase I (CBH I) was more compatible with choline phenylalaninate ([Cho][Phe]). The overall cellulase activity in [Cho][Gly] was more promising, with a 13.9 % increase in enzymatic activity. Computational findings revealed that the high flexibility of EG I's loop regions might contribute to its slightly enhanced activity in [Cho][Gly]. The slightly enhanced enzymatic performance of CBH I in [Cho][Phe] was attributed to the solvent environment rather than structural changes. Notably, the intrusion of the choline cation into the catalytic domain of EG I in [Cho][Phe] was captured, which likely caused the partial deactivation of the EG I in [Cho][Phe]. [Cho][Gly] holds considerable potential as a solvent for one-pot biomass pretreatment and enzymatic hydrolysis.