Intramolecular isomerization in pentacoordinate compounds can play an essential role for the adjustment of defined stereochemical information. Here, we present a conclusive mechanism of a stereocontrolled reaction on chiral dimethoxysilanes that opens new aspects in understanding the origin of creating silicon-centered chirality during a nucleophilic substitution process. By combining experimental, structural, and quantum chemical methods, we were able to disclose an interconversion process, based on consecutive Berry-type motions, as the most plausible mechanism for describing the stereochemical outcome in suchlike substitution reactions.