The present study addressed the influence of lithological variability on hydrothermal alteration processes in the Çubuk region of Ankara, recognized globally for its agate occurrences. The objective was to clarify how differing host rocks, tuff and ignimbrite in Karadana, and perlitic units in Yukarıemirler, affect secondary mineral formation and alteration pathways. A combination of mineralogical (X-ray diffraction, Fourier-transform infrared spectroscopy, field-emission scanning electron microscopy) and geochemical (energy-dispersive X-ray spectroscopy, whole-rock geochemistry, δ18O–δD) methods was utilized to characterize alteration assemblages and fluid conditions. The alteration sequence progressed through five stages, beginning with unaltered volcanic rocks. In the second stage, smectite-group clays, particularly montmorillonite, were formed under mildly alkaline and low-temperature conditions (pH 7.5–9.0; T 43–50°C). This initial clay formation was followed by zeolitization along two distinct pathways: clinoptilolite crystallized (K-rich, Si/Al ~4.2) in the Karadana tuff–ignimbrite units, while heulandite formed (Ca-rich, Si/Al ~2.7) in the perlitic host rocks of Yukarıemirler. These variations are attributed to differences in host-rock composition, permeability, and hydrothermal fluid chemistry. In more advanced stages, mordenite and chabazite precipitated under progressively higher pH and temperature conditions (pH 9.5–10.0; T 70–80°C). In the final stage, opal–quartz formed due to silica supersaturation triggered by a drop in pH, despite rising temperatures (pH ~8.5–9.0; T ~250°C). The paragenetic sequence confirms that clay mineral formation preceded zeolitization in both zones. Variations in zeolite types reflect strong lithological and hydrochemical controls, as well as the origin of the hydrothermal fluids; clinoptilolite formation in Karadana is associated with Na- and K-rich supergene fluids, while Ca-rich hypogene fluids promoted heulandite precipitation in Yukarıemirler. This study presents the first detailed paragenetic model for zeolite–clay alteration in the Çubuk volcanic system and offers new insights into post-caldera hydrothermal evolution in Central Anatolia.