The collagen structure in skins is significantly influenced by the cross-linking chemistry adopted during leather processing. We have developed an in situ technique to measure real-time collagen structure changes using synchrotron-based small-angle X-ray scattering (SAXS). Three common mineral tanning systems, basic chromium sulfate (BCS), zirconium sulfate (ZIR) and an aluminosilicate-based reagent (ALS) were used to stabilize collagen in ovine skin. Studying the molecular changes by in situ SAXS revealed a range of tanning mechanisms: a complex combination of covalent cross-linking, electrostatic interactions and hydrogen bonding by BCS, hydrogen bonding interactions by ZIR, and the formation of colloidal aggregates by ALS. These results unravel the mechanisms of producing leathers with different properties, explaining why ZIR produces denser leathers while ALS produces softer leathers compared to conventional BCS leathers. ZIR and ALS are environment-friendly alternatives to BCS, and understanding their mechanisms is important for a more sustainable future for the leather industry.