Many studies have improved our understanding of the mode of preservation at the Crato fossil Lagerstätte. The high degree of preservation of the Crato mineralized insects is thought to be a consequence of the diffusion of ions through carcasses and envelopment by bacteria that, in turn, created microenvironmental conditions that led to mineralization, mainly pyritization. Pyritized insects have been oxidized by in situ weathering to more stable oxide/hydroxy minerals during Quaternary time. This transformation is essential to maintain the palaeontological information acquired during microbially induced pyritization in an oxidizing atmosphere. However, intense weathering can diminish or obscure the morphological fidelity, and little attention has been paid to the post-diagenetic processes experienced by these fossils. Here, we aim to determine the degree of alteration undergone by Crato pyritized insects using the following combination of analytical tools: scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared and Raman spectroscopy. Our results show that well-preserved insects are preferentially replaced by haematite and poorly preserved fossils are replaced by goethite. In addition, we recorded three types of post-diagenetic alteration: insects with iron-oxide overgrowths; insects associated with black coatings, sometimes with the formation of dendrites; and insects preserved as an impression, where only the outline of the body remains. All of these alterations have the potential to distort or tarnish palaeontological information. Here, we measured the effects of such telodiagenetic alterations at macro and micro scales. Therefore, this taphonomic approach has wide applicability wherever fine-grained deposits bearing mineralized insects are found.