In this work a capillary electrophoretic (CE) method is used for the kinetic study of the intermetallic substitutions in hexameric ions of two strategic metals, tantalum and niobium in an alkaline medium. Recently proposed processes for the production and analytical separation of tantalum and niobium that are faster, more economical and environmental friendly are based on the use of highly alkaline media. It was previously established that in these media, tantalum and niobium exist as hexameric species, HxTa6O19X-8 (Ta6) and HxNb6019x-8 (Nb6), which can be analysed with a CE method using an alkaline electrolyte and UV detection. However, when using the above method on an industrial sample a minor species that should correspond to the substituted Ta1Nb5 form was observed. The purpose of the present study is to probe, by means of CE, the kinetic of the formation of substituted niobate-tantalate ions, Ta6-xNbx (1 ≤ x ≤ 5), starting from mixtures of pure hexaniobate and hexatantalate ions. This study required the development of a new CE method allowing the separation of all the five substituted ions and their two non-substituted hexameric parent ions in less than seven minutes. In details, a previously developed separation method was transferred to a Beckman instrument and the separation improved by adjusting the total length, the applied voltage, the injection volume, the rinsing steps and the internal standard. The kinetic study shows that samples initially containing non-substituted hexameric forms of tantalum and niobium in a 1:1M ratio naturally form the five possible substituted species Ta6-xNbx (1 ≤ x ≤ 5) after only a few hours which may represent an issue for future Nb-Ta separation processes operated in alkaline media. The developed method was also transferred to an Agilent instrument and the kinetic study repeated. Results obtained with the Agilent instrument corroborate those obtained with the Beckman instrument. The proposed electrophoretic separation method lays the ground for new analytical techniques that could help assessing the presence of substituted species that can be deleterious for Nb-Ta purification processes.