Collagen is an important biomacromolecule, making up the majority of the extracellular matrix in animal tissues. Naturally occurring crosslinks in collagen stabilize its intermolecular structure in vivo, whereas chemical treatments for introducing synthetic crosslinks are often carried out ex vivo to improve the physical properties or heat stability of the collagen fibres for applications in biomaterials or leather production. Effective protection of intrinsic natural crosslinks as well as allowing them to contribute to collagen stability together with synthetic crosslinks can reduce the need for chemical treatments. However, the contribution of these natural crosslinks to the heat stability of collagen fibres, especially in the presence of synthetic crosslinks, is as yet unknown. Using synchrotron small-angle X-ray scattering, the in situ role of natural and synthetic crosslinks on the stabilization of the intermolecular structure of collagen in skins was studied. The results showed that, although natural crosslinks affected the denaturation temperature of collagen, they were largely weakened when crosslinked using chromium sulfate. The development of synergistic crosslinking chemistries could help retain the intrinsic chemical and physical properties of collagen-based biological materials.