The potential use of near-infrared (NIR) spectroscopy as a characterization tool for organo-clays would be a great asset but little work has been done in this regard because the application of NIR to clay mineral studies is a relatively new phenomenon. The purpose of this study was to use NIR spectroscopy to investigate the effect of alkylammonium cations on the acid dissolution of a high-charge montmorillonite (SAz-1). Detailed analysis of the spectra of Li+-, TMA+- (tetramethylammonium), and HDTMA+- (hexadecyltrimethylammonium) saturated SAz-1 montmorillonite in the NIR region was achieved by comparing the first overtone (2ν) and combination (ν+δ) bands of XH groups (X = O, C) with the fundamental stretching (ν) and bending (δ) vibrations observed in the mid-infrared (MIR) region. Comprehensive analysis of the vibrational modes of CH3–N, CH3–C, and –CH2–C groups of TMA+ and HDTMA+ cations detected in the MIR and NIR regions was also performed. Both MIR and NIR spectra demonstrated that exchange of Li+ by TMA+ only slightly improved the resistance of SAz-1 layers to dissolution in 6 M HCl at 80°C, while exchange by the larger HDTMA+ cations almost completely protected the montmorillonite layers from acid attack. Use of NIR spectra in reaching these conclusions was crucial. Only in the NIR region could the creation of SiOH groups be monitored, which is an important indicator of the acidification of the montmorillonite surface. The OH-overtone region in the spectra of Li-SAz-1 and TMA-SAz-1 revealed that the SiOH band near 7315 cm−1 increases in intensity with enhanced acid treatment. In contrast, no SiOH groups were identified in the NIR spectra of HDTMA-SAz-1 treated in HCl, indicating that HDTMA+ completely covers the inner and outer surfaces of the montmorillonite and hinders access of protons to the Si–O− bonds created upon acid treatment.