Gene expression plasticity enables organisms to respond to changes in their environment. The degree to which such plasticity contributes to species’ resilience or vulnerability to change is currently unknown. Historical gene expression data spanning the last century would accelerate study of how gene expression shifts might be involved in response to climate change. Museum specimens represent phenotypic snapshots spanning the last 150 years – a period of rapid environmental change. Unfortunately, most specimens, especially those older than 20-30 years, were not preserved with molecular technologies in mind. Therefore, we must seek alternative measures to discover signatures of historical epigenetic state, which could reveal priceless long-term time-series data. Here we describe two complementary and novel approaches to estimate chromatin accessibility in formalin-preserved museum specimens. Specifically, we leveraged the widespread process of formalin preservation to enrich genome-wide sequencing data for open chromatin regions, akin to the contemporary methodology of ‘formaldehyde assisted identification of regulatory elements’ (FAIRE-seq). Secondly, we optimised micrococcal nuclease treatment in combination with the natural process of DNA degradation, to reveal nucleosome patterning. Our approach provides new capability to track the trajectory of temporal gene regulatory trends and it increases the utility of older and poorly preserved specimens, that were previously considered sub-optimal genomic resources. Estimation of historical gene activity could reveal how species have coped with past environmental change, enable predictions about future species resilience to environmental stressors and improve the accuracy of biodiversity assessment and management.