© 2020 Elsevier Ltd Cellulose nanocrystals (CNCs) were isolated from two-agroindustrial wastes: sugarcane bagasse (SCB) and pinewood sawdust (PWS), to analyze their chemical, structural, morphological, and proton conduction properties in dependence of the synthesis parameters. In both sources, the isolated CNCs correspond to the monoclinic phase of cellulose type I and II. For SCB, the smallest CNCs were isolated, in a range of 3–10 nm, with 5 wt.% of NaOH and 60 °C of acid hydrolysis. PWS displayed the smallest sizes at 75 °C and 10 wt.% NaOH (40–110 nm). Membrane characterization suggests that isolated CNCs, between 75 and 90 °C of acid hydrolysis and 10 wt.% NaOH from both SCB and PWS sources, displayed an important increase in the proton conductivity, 1.23(±0.61)×10−5 and 9.26 (±0.24)×10-5 S-m-1, respectively. Thus, with proper synthesis conditions, CNCs can be potentially used as based element to obtain other proton conductor materials to fabricate PEMs.