© 2020 The Author(s) The data shown in this document provides all the experimental data that complement the article published in Carbohydrate Polymers entitled “Influence of operating conditions on Proton Conductivity of Nanocellulose films using two Agroindustrial Wastes: Sugarcane Bagasse and Pinewood Sawdust” . The data of this paper are the result of a large series of experiments to optimize the extraction of cellulose nanocrystalline (CNC) from these two agro-industrial wastes: sugarcane Bagasse (SCB) and pinewood sawdust (PSW). The conditions of pretreatment (5 wt.% or 10 wt.% of NaOH) and hydrolysis temperature (60, 75 and 90°C) in an aqueous solution of 45 wt.% of H2SO4 were analyzed exhaustively. The data includes the characterization by Fourier transform infrared (FT-IR), Differential Scanning Calorimetry/Thermogravimetric Analysis (DSC/TGA), Dynamic Light Scattering (DLS), X-ray diffraction (XRD) patterns, Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) micrographs with their corresponding SAED patterns and nanoindentation tests. Additionally, photographs during the isolation of cellulose nanocrystalline in dependence of the syntheses parameters. It is also included the data that complement the molecular dynamic simulation generated by GLYCAM carbohydrate builder based on the coordinates for alpha and beta cellulose considering a microfibril of 5, 10 and 20 glucosyl residues (degree of polymerization, DP). Overall data have not been previously published and are available contributing to a better understanding of the CNCs isolation through different pretreatment concentrations and temperatures of processing.