Hydrothermal alteration led to development of the Yarıkçı clay deposit within the Mesozoic chlorite-, muscovite-, chlorite-muscovite-schist, and garnet-graphite phyllite units along NW–SE- and N–S-trending faults in Mihalıççık in western central Anatolia. The geological, mineralogical, and geochemical characteristics and genesis of this economically important clay deposit have not been examined in detail previously. The present study has attempted to fill this gap. Green smectitic and cream kaolinitic claystones are abundant with smaller amounts of gray illite, dark brown Fe oxides, and silica phases occurring as stockwork/fracture infill and stain/coating. These units are covered by a dark, hard, sharp-edged, and thick silica cap. Metamorphic units exhibit cataclastic texture due to tectonic activities. Muscovite is mostly degraded to kaolinite, and feldspars show sericitization and argillization. Kaolinite typically has a platy form with irregular margins and locally sub-rounded, book-like texture suggesting hydrolysis during the hydrothermal injections. The association of Fe oxides, cristobalite/tridymite/quartz, gypsum/anhydrite, and jarosite are indicative of intense hydrothermal activities and development of kaolinite under acidic geochemical conditions. The local enrichment of SiO2, Fe2O3, S, Cu, and Au also supports this suggestion. The leaching of Sr, Rb, Ba, and Zr, and the slight increase in LREE/MREE+HREE ratios together with the negative Eu and Ce anomalies suggest the selective dissolution of muscovite, garnet, feldspar, and pyroxene by the hydrothermal fluids. Thus, abundant claystones of smectite and kaolinite were formed via the increase in Al+Fe+Mg/Si and Al±Fe/Si ratios in the alkaline and acidic environment, respectively, under the tectonic control of hydrothermal activity as seen in the alteration of chlorite, muscovite, and feldspar in metamorphic units.