<p>Wildlife persistence in human-modified landscapes is often inferred from habitat use, yet this assumption may overlook critical life-history constraints such as access to secure resting refuges. Using long-term Very High Frequency telemetry of eight sympatric Sunda pangolins (<i>Manis javanica</i>) in a forest–oil palm plantation mosaic in Sabah, Malaysia, we quantified denning range size, spatial overlap, sleeping site use, and reuse to evaluate how fine-scale refuge use structures space use. Denning range size and spatial overlap did not differ between forest-only and mixed forest–plantation individuals, indicating that macrohabitat context alone did not constrain denning spatial organisation. However, pangolins disproportionately used structurally enclosed sleeping sites such as tree hollows and burrows, while plantation use was largely restricted to exposed palm crowns that exhibited the lowest reuse rates. Sleeping site reuse probability was higher in forests than in plantations and was primarily structured by microhabitat type. These results demonstrate a decoupling between habitat use and functional habitat suitability, whereby animals may occupy modified landscapes while remaining dependent on a limited set of structurally stable refuges. Conservation strategies in agricultural landscapes should therefore prioritise the retention and restoration of structurally complex refuges, rather than relying solely on habitat extent or connectivity, to avoid overestimating functional habitat suitability for shelter-dependent species.</p>