<p><i>Linum mucronatum</i> subsp. <i>gypsicola</i> is an endemic species of Linaceae, restricted to gypsum-marl hills in northwestern Türkiye. This study examines in detail the micromorphological and ecological adaptations of the gypsophyte <i>L. mucronatum</i> subsp. <i>gypsicola</i>, which survives in arid and gypsum soils. Light microscopy (LM), scanning electron microscopy (SEM), scanning electron microscopy coupled with energy-dispersive X-ray (SEM–EDX) analyses, multi-elemental analyses, and soil analyses were performed on the vegetative parts of the plant to obtain valuable data on how the plant survives in this challenging environment. Microscopic examinations revealed important micromorphological features such as the developed secondary xylem layer in the roots, the narrowed pith region of the stem, the high stomatal density in the leaves, the amphistomatic structure, the arrangement of palisade parenchyma cells, and the thin and loose structure of the sponge parenchyma. Multi-elemental analyses detailed the accumulation of macro and micronutrients in the vegetative tissues of the plant and clarified the effects of these elements on plant development. In addition, these analyses revealed how the plant responds to substrate-derived nutrients. The microscopic and phytochemical analysis findings significantly contribute to our understanding of the adaptations that allow <i>L. mucronatum</i> subsp. <i>gypsicola</i> to survive in extreme habitats.</p> Graphical Abstract <p></p>