Co-ordinated regulation of chromatin architecture is a major driver of phenotypic diversity, development and disease but we know shockingly little about the evolutionary dynamics of chromatin reorganisation as it has occurred through time. Linking the disparate fields of chromatin biology and museum science by their common use of the preservative formaldehyde, we characterise the first genome-wide historical chromatin profiles in formalin-fixed museum specimens up to 117 years old. Over-fixation modulates but does not eliminate genome-wide patterns of differential chromatin accessibility and enables semi-quantitative estimates of relative gene expression. Our methodological and analytical advances open the door to the first detailed and comprehensive view of the epigenetic past and reveal a new role for museum collections in understanding chromatin architecture dynamics over the last century.