We assessed the impact of fog on microclimate in a poorly understood fog desert under two common nurse plant species, at three sites: (1) foggy coast, (2) intermediate, and (3) above the main fog belt in the Atacama Desert (Peru). We quantify nurse plant modification of their understory that creates favorable microsites for other species. Dataloggers collected temperature, relative humidity (RH) and dew point temperature under Randia armata, Caesalpinia spinosa and in the open at the three sites. The Relative Interaction Index (RII), Friedman’s two-way ANOVA, and correlation were used to compare conditions across microsites and field sites. At noon, the understory was cooler and RH was higher than in the open, consistent with non-fog deserts. Early morning temperatures were warmer in the open at the more fog-influenced sites, unlike non-fog deserts. The temperature gap (cooler in the understory) is smallest at the coast and largest in the interior. Temperature and moisture generally fluctuate less at the most fog-influenced sites, while understory conditions at the interior (least-fog influenced) site was most similar to those found in non-fog deserts. Because fog reduces weather extremes, amelioration by vegetation becomes less on foggy days as extremes are already dampened by the fog, and facilitation by nurse plants is greatest when conditions are most like traditional deserts (e.g., clear skies, hot). These results provide mechanistic support for the effects of nurse plants through stress amelioration in fog deserts.