<p>Monitoring elusive, low-density species requires efficient, cost-effective methods that minimise human effort while ensuring reliable detection. This study evaluated the effectiveness of footprint tunnels compared to long-term nest box monitoring in detecting hazel (<i>Muscardinus avellanarius</i>) and garden (<i>Eliomys quercinus</i>) dormice. During 2022, we conducted 15 monitoring sessions across six areas (1,200–1,966&#xa0;m a.s.l.) in the Western Alps, using 217 paired nest boxes and footprint tunnels, collecting 2,015 footprint cards and recording 126 hazel dormice and 27 garden dormice in nest boxes. Single-season occupancy models incorporating method as an observation-level covariate showed that footprint tunnels consistently outperformed nest boxes in detecting both hazel and garden dormice. Detection probabilities were approximately eight times higher for hazel dormice when using footprint tunnels, both during the peak period from the second half of July to the second half of September and across the other sampling intervals, and even higher for the garden dormouse. Moreover, footprint tunnels yielded a stable frequency of occurrence from May to December, while nest boxes showed delayed or lower occurrences. Although footprint tunnels may be susceptible to environmental interference, lower disturbance and reduced effort requirements make them a preferred method for large-scale dormouse detection. While less efficient for presence/absence surveys, nest boxes remain necessary for demographic studies involving the handling of animals. Our results indicate that footprint tunnels provide a reliable and low-effort ethical alternative that supports monitoring practices, as already shown by previous studies, and strengthens compliance with the EU Habitats Directive, thereby advancing dormouse conservation outcomes in line with the principles of Replacement, Reduction, and Refinement.</p>