Nowadays, metakaolin is currently widely used as a supplementary cementitious material in the concrete industry. However, there are significant differences between kaolinitic clays, which can be used for the production of metakaolin. They can vary in the granulometry as well in the mineralogical composition (more precisely the content of varying impurities can differ widely). The main aim of this article is to assess the impact of mentioned variation on the thermal activation of such kaolinitic clays. For this purpose, four clays from the Czech Republic were chosen and examined. Primarily, their characterization composed of XRD, DSC, granulometry, and specific surface area was studied. Then these clays were thermally activated at temperatures from 500°C to 650°C. Afterwards, the changes in determined properties were investigated. Then the samples of blended cement pastes with a replacement level of 15% were produced, and basic physical and mechanical properties were determined. It was proved that for particular clays, different temperature treatments were optimal, which further lead to varying results of the mechanical performance of blended cement-based pastes. Such variation can be linked to the phase composition of studied clays.