This study delves into the acid modification of natural zeolite clinoptilolite, focusing on the identification of acid site types and their catalytic activity in the Brønsted acid‐catalyzed acetalization of benzaldehyde with 1,3‐butanediol. Following calcination, the samples underwent acidification via ammonium‐ion exchange, resulting in approximately 45% of the clinoptilolite cations being exchanged with ammonium ions. The investigation evaluates the structural, morphological, and textural alterations induced by this modification using XRD, FTIR, and nitrogen adsorption‐desorption measurements. Ammonia‐temperature‐programmed desorption (NH3‐TPD) analysis confirms the presence of medium to strong acidic protons, highlighting the acidity of the modified samples. Employing 27Al and 29Si magic‐angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy elucidated changes in the state and coordination of aluminum post‐sample activation. Specifically, the 27Al MAS NMR spectra indicate a partial dealumination, evidenced by the emergence of 5 and 6‐fold coordinated aluminum. Moreover, 29Si MAS NMR measurements tracked variations in the Si/Al ratio. The study probes the nature of these sites, their influence on catalytic activity, and the synergistic interplay between Brønsted acid sites and 5‐fold coordinated aluminum. The results showcase that the prepared acidic natural clinoptilolite catalysts augment acidity and porosity, fostering promising implications for catalytic applications.