Phosphorus contained in atmospheric mineral dust aerosol originating from Africa fertilizes tropical forests in Amazonia. However, the mechanisms influencing this nutrient transport pathway remain poorly understood. Here we use the Community Earth System Model to investigate how large-scale deforestation affects mineral dust aerosol transport and deposition in the tropics. We find that the surface biophysical changes that accompany deforestation produce a warmer, drier, and windier surface environment that perturbs atmospheric circulation and enhances long-range dust transport from North Africa to the Amazon. Tropics-wide deforestation weakens the Hadley circulation, which then leads to a northward expansion of the Hadley cell and increases surface air pressure over the Sahara Desert. The high pressure anomaly over the Sahara, in turn, increases northeasterly winds across North Africa and the tropical North Atlantic Ocean, which subsequently increases dust transport to the South American continent. We estimate that the annual atmospheric phosphorus deposition from dust significantly increases by 27% (P < 0.01) in the Amazon under a scenario of complete deforestation. These interactions exemplify how land surface changes can modify tropical nutrient cycling, which, in turn, may have consequences for long-term changes in tropical ecosystem productivity and biodiversity.