Biological nitrogen fixation is critical for the nitrogen cycle of tropical forests, yet we know little about the factors that control the microbial nitrogen-fixers that colonize the microbiome of leaves and branches that make up a forest canopy. Forest canopies are especially prone to nutrient limitation because they are (1) disconnected from soil nutrient pools, and (2) often subject to leaching. Earlier studies have suggested a role of phosphorus and molybdenum in controlling biological N-fixation rates, but experimental confirmation has hitherto been unavailable. We here present the results of a manipulation of canopy nutrient availability . Our findings demonstrate a primary role of phosphorus in constraining overall N-fixation by canopy cyanobacteria, but also a secondary role of molybdenum in determining per-cell fixation rates. A conservative evaluation suggests that canopy fixation can contribute to significant N fluxes at the ecosystem level, especially as bursts following atmospheric inputs of nutrient-rich dust.