Terraces near Flamencos Lagoon in the southeastern Salar de Pajonales (Chile), located at 3,517 m above sea level in the arid Altiplano, host relic gypsum stromatolites and crusts formed under extreme desiccation, intense solar radiation, and episodic hydration. These gypsum-rich environments provide a natural analog for Martian evaporitic settings, where habitability and biosignature preservation may coexist. By combining meteorological, geochemical, isotopic, and microbiological data from 19 gypsum-dominated microhabitats, we identified strong environmental controls on mineral formation and microbial community structure. The gypsum evaporitic systems of the Salar de Pajonales preserve both molecular and morphological biosignatures while sustaining microbial life under extreme conditions. The spatial separation between fossil and extant signatures underscores gypsum’s exceptional capacity to entomb and protect biological evidence, reinforcing its importance as a prime target for astrobiological exploration on Mars.