Concentrated protic ionic liquid (PIL) without dilution has increased saccharification efficiency due to the solubilization of hemicellulose and lignin compounds. However, concentrated PILs are not cost-effective, highly viscous, and toxic to microorganisms. The present study evaluates the effect of PILs on the solubilization of hemicellulose and lignin present in coconut coir and pith. PILs including pyridinium hydrogen sulfate [PyH][HSO4] and triethylammonium hydrogen sulfate [TEA][HSO4] were considered in this study. The sugars and lignin were partially hydrolyzed during the PIL pretreatment of coir and pith. However, the degree of biomass solubilization varied for different types of biomass and PIL. The changes in the biomass after pretreatment were studied through FTIR and XRD analysis. The yield of glucose released from [PyH][HSO4] and [TEA][HSO4] pretreated coir and pith increased 4.12, 4.73 and 7.36, and 6.44, respectively. The results showed that diluted PIL could be used in a biorefinery to increase the glucose yield with almost similar efficiency obtained from concentrated PIL. The recovery and reusability studies showed the recycled PIL could be utilized 3 times. Further application of low concentrations of PIL suggests the possibility of a new process design for a biorefinery to achieve low operating costs. Graphical abstract[Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.