Extremely narrow endemic plant species (ENEs) are generally connected with microrefugia characterized by particular environmental conditions. In-depth knowledge of the ecological requirements of ENEs is fundamental to plan appropriate conservation measures. Using cross-cutting technology, this paper gives a multifaceted approach to collect on-site data on the ecology of ENEs, defines the protocols for a correct sampling design and describes the type of equipment, the time and expenditure needed. Our sampling approach is based on two orthogonal transects, long enough to extrapolate the whole ecological gradient across the area of occupancy of the target species. Microclimatic data are recorded all along the transects through iButton technology, plus a weather station installed at the intersection of the transects. Microtopographic data are recorded with high-resolution digital elevation model and sub-metric GPS. Edaphic data are recorded along the transects through standard soil analyses and on-site evaluation of the seasonal decomposition rate of organic matter. Additionally, vegetation sampling in 4m2 plots and on-site germination tests allow to collect data on auto- and synecological factors that regulate the life cycle of the target species. Our approach has proved to be cost-effective and efficient in terms of time spent in the field against the data collected. The most demanding activities were the establishment of the transects and the vegetation sampling. The time spent downloading microclimatic data and testing seed germination was relatively short. Our sampling design allows: (i) to catch as much micro-topographic variability as possible, both within and out of the tolerance range of the target species, (ii) to minimize the risk of recording identical micro-topographic conditions compared with a random sampling scheme, and (iii) to ensure quick and relatively easy retrieval of the plots and the equipment both on a multi-seasonal and multi-annual basis.