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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. Here we 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 …