Deposition of dust particles on plant leaves reduces light interception. Additionally, dust accumulation in stomata decreases gas exchange in leaves. The effects of dust deposition following sand and dust storms (SDS) are critical, and the physiological responses of plants to dust deposition as an abiotic stress factor are of primary importance. We hypothesized that dust storm occurrence negatively affects leaf traits in wheat (Triticum aestivum L.) and cowpea (Vigna unguiculata L.). The effects of desert dust on photosynthetic pigment contents and stomatal conductance were studied in both species. Wheat and cowpea plants were subjected to dust treatments in a factorial layout based on a randomized complete block design in Dezful and Mashhad. Experimental treatments included desert dust concentration (0, 500, and 1500 µg m⁻³), number of dust applications (once, twice, thrice), and dust type (samples collected during dust storms in Dezful and Zabol, two of the most dust-prone regions of Iran). Dust application reduced stomatal conductance in both plants at both locations. Increasing dust concentration reduced chlorophyll a+b, a, and b in wheat leaves, while only chlorophyll b in cowpea leaves was significantly affected. Overall, this study provides new insights into how desert dust affects photosynthetic pigments and stomatal conductance in wheat and cowpea through shading and stomatal occlusion during dust storms.