In this work, we report the preparation, isolation, and characterization of a family of double-decker silsesquioxane architectures starting from the previously reported DDSQ-Me₂H₂ precursor, a mixture of cis and trans isomers. Using such a starting material results in a subsequent mixture of isomers when hydrosilylation reactions using DDSQ-Me₂H₂ and hydroxyalkyl-substituted alkenes catalyzed by Karstedt catalyst are performed. We describe a procedure to sequentially crystallize the two isomers from one another, affording a protocol potentially applicable to other closely related derivatives. The ability to access pure cis and trans isomers of double-decker silsesquioxanes may result in the preparation of new materials and polymers with well-defined properties. All resulting silsesquioxanes were characterized by multinuclear (¹H, ¹³C, and ²⁹Si) NMR spectroscopy, FT-IR, and HR-MS. Additionally, we report five crystal structures of geometrical isomers, including two cis forms described in the literature for the first time. This is a breakthrough in itself and sets a new strategy for obtaining such exiting organosilicon-based systems.