The extraction of environmental DNA (eDNA) from sediments is providing ground-breaking views of past ecosystems and biodiversity. Despite this rich source of information, it is still unclear which sediments favor preservation and why. Here, we used atomic force microscopy and molecular dynamics simulations to explore the DNA-mineral interaction to assess how mineralogy and interfacial geochemistry play a role in the preservation of environmental DNA on mineral substrates. We demonstrate that mineral composition, surface topography, and surface charge influence DNA adsorption behavior as well as preservation. Modeling and experimental data show that DNA damage can be induced by mineral binding 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 assessing if a deposit is capable of storing extracellular DNA and to what extent the DNA would be preserved. Our data adds to the understanding of eDNA taphonomy and highlights that, for some mineral systems, fragmented DNA may not represent old DNA.