The Late Messinian fill of the Nijar Basin (Betic Cordillera, southeastern Spain) mainly consists of clastic deposits of the Feos Formation that at basin margins rest unconformably above the primary evaporites of the Yesares Formation, the local equivalent of the Mediterranean Lower Gypsum. The Feos Fm. records the upward transition towards non-marine environments before the abrupt return to fully marine conditions at the base of the Pliocene. The Feos Fm. is clearly two-phase, with ‘lower’ and ‘upper’ members, which exhibit substantial differences in terms of facies, thickness, depositional trends and cyclical organization. These members record two distinct sedimentary and tectonic stages of Nijar Basin infilling. A high-resolution, physical-stratigraphic framework is proposed based on key beds and stratigraphic cyclicity and patterns that differ largely from those of most previously published studies. The predominant influence on stratigraphic cyclicity is interpreted to be precessionally driven climate changes, allowing their correlation to the Late Messinian astronomically calibrated chronostratigraphic framework. Detailed correlations suggest a phase of enhanced tectonic activity, possibly related to the Serrata-Carboneras strike-slip fault zone, during the first stage (‘lower’ member), resulting in a strongly articulated topography with structural lows and highs controlling sediment thickness and facies variation. Tectonic activity decreased during the second stage (‘upper’ member), which is characterized by (1) a progressively dampened and homogenized, (2) overall relative base-level rise and (3) gradual establishment of hypohaline environments. Facies characteristics, overall stacking patterns and depositional trends of the Feos Fm. are analogous with uppermost Messinian successions of the Northern Apennines, Piedmont Basin and Calabria. Despite minor differences related to the local geodynamic setting, these basins experienced a common Late Messinian history that supports the development of a single, large Mediterranean water body characterized by high-frequency, climatically-driven changes in sediment flux and base-level.