Clay minerals are key indicators of soil evolution and the building blocks of soil behavior. Long-term agronomic trials, in which soil samples have been collected and archived over several decades, provide a valuable opportunity to track the transformation of clay minerals over centennial timescales. To achieve this, the clay mineralogy of the archived soil samples must be characterized in great detail. In this context, the initial clay mineralogy of the <2 μm fraction of one of the world’s oldest experimental sites, the 42 plots of Versailles (France, 1929), was determined using an approach that coupled sequential fractionation with X-ray diffraction profile modeling of 00ℓ reflections. This analysis of the original clay mineralogy confirmed the great complexity of temperate soil clay mineralogy. Seven clay phases were identified, including two quasi-discrete kaolinite and illite phases, and five randomly mixed-layered minerals (MLMs), three of which had three different 2:1 layer types. Results showed that MLMs accounted for >70% of the clay phases, with their proportions increasing as particle sizes decreased. The widespread occurrence of kaolinite-illite MLMs and three 2:1 component MLMs in temperate loess soils was also assessed. Comparisons with previous descriptions of clay mineralogy in temperate soils demonstrated that despite their complex crystal structures, the three 2:1 MLMs exhibited similar relative contributions from their constituent layers, particularly the illite layers. The high proportions of such illitic clay phases quantified in the study suggested that they could serve as key markers in the study of pedogenesis in soils that have developed from sedimentary rocks or deposits under temperate climatic conditions.