Epigenetic ageing in a human context, has been used to better understand the relationship between age and factors such as lifestyle and genetics. In an ecological setting, it has been used to predict the age of individual animals for wildlife management. Despite the importance of epigenetic ageing in a range of research fields, the assays to measure epigenetic ageing are either expensive on a large scale or complex. In this study, we aimed to improve the efficiency and sequencing quality of an existing epigenetic ageing assay for the Australian Lungfish (Neoceratodus forsteri). We used an enzyme-based alternative to bisulfite conversion to reduce DNA fragmentation and evaluated its performance relative to bisulfite conversion. We found the sequencing quality to be 12% higher with the enzymatic alternative compared to bisulfite treatment (p-value < 0.01). This new enzymatic based approach, although currently double the cost of bisulfite treatment can increases the throughput and sequencing quality. We envisage this assay setup being adopted increasingly as the scope and scale of epigenetic ageing research continues to grow.