Extraction of environmental DNA from sediments are providing ground-breaking views of the past ecosystems and biodiversity. Despite this rich source of information, we do not yet know much about which sediments favour preservation and why. Here we used atomic force microscopy and molecular dynamics simulations to explore the DNA-mineral binding in order to access the role of mineralogy for preservation of environmental DNA. We demonstrate that mineral composition, surface topography and charge influence DNA preservation and that damage patterns can be affected by the mineralogy, especially if there is a strong driving force for adsorption. The study shows that knowledge of the mineralogical composition of a sediment and the environmental conditions can be useful for both assessing the DNA preservation potential in a deposit as well as in interpreting extracted damage patterns. The dependence on the mineralogy for DNA preservation raises the question of whether the DNA we retrieve is merely a function of the minerals and their chemical history rather than of the past biodiversity.