—Although several hypotheses for the formation of glauconite have been proposed, the sedimentary environment and mechanism of glauconitization are still poorly understood. In this contribution, the mineralogy and chemical compositions of sediments from Paleogene formations (Fms) in the Kyzyltokoy basin (Kyrgyzstan) were examined to better understand glauconitization processes. The samples were analyzed using microscopic petrography, X-ray diffraction (XRD), electron probe microanalysis (EPMA), and X-ray fluorescence (XRF). Interlayered diatomite-argillaceous rocks were newly identified within the diatomites of the Isfara Fm. Glauconite from the Kyzyltokoy basin displayed two stages of maturity: 1) early stage (nascent) glauconite grains composed of ~3.5% K2O and ~8%FeOT; 2) late-stage (highly evolved) glauconite grains composed of 7–9% K2O and ~27% FeOT. The early stage glauconite grains in the Hanabad Fm green clay (green clay is clay with a greenish color) indicate interruptions in glauconitization processes, whereas the (highly) evolved glauconite grains show a completed glauconitization process along the contact between the Hanabad and Sumsar Fms. Hematite was detected in the red clay (clay with reddish color) of the Sumsar Fm and probably formed by glauconite disintegration. Accordingly, the Paleogene Fms depositional conditions were of three types: 1) beginning of glauconitization with interruptions, 2) completion of glauconitization, and 3) glauconite disintegration. Glauconitization in the Kyzyltokoy basin, thus, likely occurred via a combination of dissolution, precipitation, and recrystallization processes.