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Abstract Aeolian sediment transport occurs as a function of, and with feedback to ecosystem changes and disturbances. Many desert grasslands are undergoing rapid changes in vegetation, including the encroachment of woody plants, which alters fire regimes and in turn can change the spatial and temporal patterns of aeolian sediment transport. We investigated aeolian sediment transport and spatial distribution of sediment in the surface soil for 7 years following a prescribed fire using a multiple rare earth element (REE) tracer‐based approach in a shrub‐encroached desert grassland in the northern Chihuahuan desert. Results indicate that even though the aeolian horizontal sediment mass flux increased approximately three‐fold in the first windy season in the burned areas compared to control areas, there were no significant differences after three windy seasons. The soil surface of bare microsites was the major contributor of aeolian sediments in unburned areas (87%), while the shrub microsites contributed the least (<2%) during the observation period. However, after the prescribed fire, the contribution of aeolian sediments from shrub microsites increased considerably (∼40%), indicating post‐fire microsite‐scale sediment redistribution. The findings of this study, which is the first to use multiple REE tracers for multi‐year analysis of the spatial and temporal dynamics of aeolian sediment transport, illustrate how disturbance by prescribed fire can influence aeolian processes and alters dryland soil geomorphology in which distinct soils develop over time at very fine spatial scales of individual plants.