The aim of this study was to degrade proteins in high-total dissolved solids (TDS)-containing wastewater produced during the soaking process in tanneries (tannery-TDS wastewater) using a halotolerant protease-assisted nanoporous carbon catalyst (STPNPAC). A halotolerant protease was obtained from the halophile, Lysinibacillus macroides, using animal fleshing as the substrate. The protease was immobilized using ethylene diamine (EDA)/glutaraldehyde functionalized nanoporous activated carbon (EGNPAC). The optimum conditions for the immobilization of protease were determined as time (120 min), pH (6), protease concentration (575–600 U/g), EGNPAC size, salinity, and temperature (30 °C). The immobilization was confirmed by FTIR, TGA-DSC, SEM, and XRD analyses. The adsorption kinetics was consistent with a pseudo first order rate constant of 1.43 × 10−2 min−1. The thermodynamic parameters (ΔG, ΔH, and ΔS) confirmed the effective immobilization of the protease onto EGNPAC. STPNAPC was found to efficiently degrade the proteins in tannery-TDS wastewater, with a complete fragmentation time of 90 min at pH 6 and 30 °C. Accordingly, the protein fragmentation was confirmed by UV-visible and UV-fluorescence spectroscopy, ESI-mass spectrometric analysis and circular dichroic studies. The formation of protein hydrolysates was confirmed by cyclic voltammetry and electrical impedance studies. BOD5: COD value, 0.426 of treated tannery-TDS wastewater may favor sequential biological treatment processes.