Chalcedony forms across a wide area in eastern Iran, particularly in the Sarbisheh district near Birjand city, with notable occurrences in the Qazdez-Bahamarz region. Here, cryptocrystalline quartz is found in hydrothermal veins and veinlets within volcanic rocks hosted by carbonate and intermediate igneous formations. Chalcedony samples of various colours—black, purple, green, blue, lavender, grey, lemon yellow and white—were analysed using diverse techniques. These chalcedony samples display fibrous and granular textures, comprising microcrystalline quartz, cryptocrystalline moganite, and opal-CT and opal-C interlayers. Elements that affect the colouration of chalcedony include iron (producing red and yellow tones), chromium (green), manganese (black, blue and grey patterns), nickel (purple) and copper (also purple). Altered carbonate host rocks are enriched in Fe, Cu, Zn and Cd, with Al and Mn depletion. Stable isotope analyses show δ18O values in agates range from +14.9‰ to +25.5‰, whereas δ18O and δ13C values in carbonate minerals and chalcedony range from +14.1‰ to +24.8‰ and –5.7‰ to +0.7‰, indicating agate formation from mantle-derived hydrothermal fluids mixed with meteoric waters. Raman spectroscopy detected moganite, α-quartz, goethite, aragonite and illite in agate interlayers. Analyses by field-emission scanning electron microscopy (FE-SEM) and energy dispersive X-ray spectroscopy (EDS) revealed minerals of Fe, Cr, Ni, Ti and Sn. X-ray diffraction confirmed chalcedony, moganite and opal-CT, whereas EPR spectroscopy showed strong magnetic backgrounds from goethite and silicon-vacancy centres formed by radioactive decay of U, Th and their byproducts.