A semi-permanent stratocumulus-topped boundary layer (STBL) is advected daily from the Southeast Pacific toward the Atacama Desert, producing coastal fog that represents a potential water input for ecosystems and communities in this hyper-arid region (∼1 mm yr<sup><span>−</span>1</sup>). The STBL is maintained by the balance between synoptic-scale subsidence and entrainment of dry, warm air, driven by cloud-top radiative and evaporative cooling, and surface fluxes over sea and land. These processes are well studied over the open ocean, but their evolution across the ocean-to-desert transition remains poorly understood. Here, we quantify cloud cover fraction (CCF) and STBL height tendency across the Pacific-Atacama Desert transition (from ∼500 km offshore to ∼50 km inland) using three years (2022–2024) of GOES satellite and ERA5 reanalysis, with a zero-order discontinuity approach and dry-cloud formulation. Our results show that CCF decreases from offshore (0.71) to inland (0.12), with higher values in winter (0.12–0.75) than in summer (0.09–0.57). Oceanic CCF variability spans days to weeks, whereas inland CCF variability is dominated by a strong diurnal cycle. The STBL height tendency shifts from near-equilibrium between processes offshore, with a weak positive tendency (∼0.5 cm s<sup><span>−</span>1</sup>) driven mainly by cloud-top radiative cooling (∼58 %), to a strongly perturbed inland regime (∼3 cm s<sup><span>−</span>1</sup>), where surface fluxes contribute mainly to entrainment in summer (∼43 %) and to subsidence in the other seasons (∼47 %). These results show how subsidence and entrainment govern STBL persistence and breakdown across the coastal desert, with implications for ecosystems and regional climate.