In the Pacific, the protection of coral reef resources is often achieved through the implementation of village-based marine reserves (VBMRs). While substantial fisheries benefits are often reported, results of quantitative approaches are controversial for benthic macroinvertebrates, whose life history traits may cause low congruence with protective measures implemented at non-ecologically relevant scales. This study investigated the structural and behavioral responses of the exploited topshell Tectus niloticus within a very small (0.2 km2) VBMR in Vanuatu, south Pacific. The results of underwater surveys and a nine-month tagging experiment emphasized contrasted, scale-dependent responses. At the reserve scale, our results failed to demonstrate any positive effect of protection after three years of closure. In contrast, abundance, density and biomass increased more than ten-fold in the southern part of the reserve, along with significantly larger (25%) individual sizes. The dispersal of tagged specimens was also consistently lower after 2, 4 and 9 months in the latter zone. Analyses of 17 substratum variables revealed a marked small-scale patchiness delineating contrasted benthic microhabitats, the distribution of which closely matched that of trochus. We advocate that i) VBMRs have inherently unequal ecological potentials for protecting and managing highly habitat-dependent species such as trochus; ii) 'success' or 'failure' is to a certain extent pre-determined by the trajectory of species-specific microhabitats, which may outreach protection effects. This has strong implications in the Pacific where the location and size of reserves primarily depends upon marine tenure, and communities have little flexibility in setting reserve boundaries.