In this work, we evaluated the biological and geological contributions to the formation and preservation of the oxidation zones in Ľubietová-Podlipa, Ľubietová-Svätodušná, Poniky-Farbište and Špania Dolina-Piesky. This case study highlights the importance of the biological contribution to weathering processes of ore deposits. It may be extended to other similar sites in order to assess the magnitude of biological input. Using U-Pb dating, secondary minerals from Podlipa were dated to 22 ± 6 and 19 ± 4 Ma (Lower Miocene). At this time, this region experienced deep weathering under a humid and warm climate and tectonic quiescence. The isotopic (O, H) composition of the secondary minerals shows that they formed from Lower Miocene meteoric water under surface temperatures. The δ13CPDB values in malachite (–19 to –17‰) document a biological source of C, from soil CO2. The δ18OVSMOW values of the PO4 groups in the accessory fluorapatite in the host rocks (1.8 ± 1.7‰, 1σ) and pseudomalachite in the oxidation zone (12.1 ± 2.9‰, 1σ) show substantial biological P input into the oxidation zone. A biogenic source of both C and P agrees well with the palaeoclimatic constraints based on the radiometric dating. The oxidation zones at Podlipa, Svätodušná and Farbište are contemporaneous with kaolin crusts in the same area; they were all preserved only where they were covered by young (14–12 Ma) volcanic rocks and exposed recently by erosion. The other oxidation zones in the Tatric and Veporic units, if they existed, were destroyed by the Pliocene uplift of these units. The oxidation zone at Piesky is younger, dated to 2.5 Ma (Early Pleistocene) when the global temperatures in interglacials were similar to the present, decreasing in glacials by ∼4°C. The different climate at this time is manifested by scattered δ13C values, reflecting surface temperature and vegetation fluctuations at this time.