Systematic periodic density functional theory computations including dispersion correction (DFT-D) were carried out to determine the preferred location site of Zr atoms in sodalite (SOD) and CHA-type topology frameworks, including alumino-phosphate-34 (AlPO-34) and silico-alumino-phosphate-34 (SAPO-34), and to determine the relative stability and Brönsted acidity of Zr-substituted forms of SOD, AlPO-34, and SAPO-34. Mono and multiple Zr atom substitutions were considered. The Zr substitution causes obvious structural distortion because of the larger atomic radius of Zr than that of Si, however, Zr-substituted forms of zeolites are found to be more stable than pristine zeolites. Our results demonstrate that in the most stable configurations, the preferred favorable substitutions of Zr in substituted SOD have Zr located at the neighboring sites of the Al-substituted site. However, in the AlPO-34 and SAPO-34 frameworks, the Zr atoms are more easily distributed in a dispersed form, rather than being centralized. Brönsted acidity of substituted zeolites strongly depends on Zr content. For SOD, substitution of Zr atoms reduces Brönsted acidity. However, for Zr-substituted forms of AlPO-34 and SAPO-34, Brönsted acidity of the Zr-O(H)-Al acid sites are, at first, reduced and, then, the presence of Zr atoms substantially increased Brönsted acidity of the Zr-O(H)-Al acid site. The results in the SAPO-34-Zr indicate that more Zr atoms substantially increase Brönsted acidity of the Si-O(H)-Al acid site. It is suggested that substituted heteroatoms play an important role in regulating and controlling structural stability and Brönsted acidity of zeolites.