Despite their impacts on ecosystems, climate, and human health, atmospheric emissions of mineral dust from deserts have been scarcely studied. This work estimated dust emission flux (E) between 1979 and 2014 from two desert regions in the Baja California Peninsula (BCP) using a modified dust parameterization scheme. Subsequently, we evaluated the processes controlling the variability of E at intra- and interannual scales. During the period 1979–2014 peak E were generally recorded in summer (San Felipe) and spring (Vizcaino), and the lowest emissions occurred in autumn (San Felipe) and winter (Vizcaíno). Intra- and interannual variability in E was associated with fluctuations in wind speed and direction, precipitation, and soil moisture, which, in turn, were controlled by the seasonal displacement of the North Pacific high-pressure center. Key drivers of the interannual variability of E are strong El Niño Southern Oscillation (ENSO) events. These climatic events and the hydrometeorological variables mentioned above played a major role in the onset and occurrence of dust events, with the highest annual emissions at Vizcaíno. Besides, a lag of 19 months (San Felipe) and 21 months (Vizcaino) was recorded between the occurrence of relevant E and ENSO events, apparently in response to the effect of this climatic event on precipitation. The climate variability of E in both desert regions was evidenced by the positive trends associated with increases in wind speed and air temperature, and with decreases in precipitation and soil moisture. Finally, our findings suggest that the BCP should be considered as a significant source of dust for the regional inventory of particulate matter emissions from the Earth’s surface.