Wind-blown sand and dust emissions shape singular landscapes in arid environments and globally impact climate, life and human activities. However, the accurate quantification of aeolian sediment fluxes are still subject to considerable uncertainties. Since extensive measurements are difficult to implement in the field, this quantification rely essentially on remote sensing data and transport laws that integrate a large number of parameters for the airflow and granular bed. However, confronted with all the sources of natural variability (wind regime, air recirculation, grain-size distribution, soil composition, etc.), a complete mass balance of aeolian transport remains challenging. Here we consider long time scales to smooth out such variability and integrate arid landscape dynamics into the source-to-sink assessment of aeolian mass transfers in the Lut Desert (Iran). Taking advantage of new remote sensing imagery and dating techniques, together with more accurate wind data and a deeper understanding of dune dynamics, we analyze major landforms of this desert to provide a comprehensive picture of aeolian transport on time scales from decades to millions of years. We map the modern sandflows, along which we evaluate the volume and chronology associated with the excavation of mega-yardangs upwind and the formation of giant dunes downwind. Sediment discharges deduced from long-term erosion and deposition are of the same order of magnitude (105 to 106 m3yr-1) as short and medium-term sand discharges derived from wind data and dune morphodynamics. At the scale of the internal aeolian sediment-routing system of the Lut, we establish an overall sediment budget constrained by the joint development of the erosional and depositional landforms. Our findings thus quantify the geomorphic controls of aeolian processes on arid landscapes at multiple length and time scales, while providing information on mass exchanges between continents and atmosphere.