Diatoms are prominent eukaryotic photoautotrophs in today’s oceans. While dominant in nitrate-rich conditions, they face competitive exclusion by other phytoplankton when ammonium forms the bulk of bioavailable nitrogen. The extent to which this competitive exclusion defines diatom abundance worldwide and the consequences of potential future ammonium enrichment remain unexplored and unquantified. Here, using phytoplankton abundance proxies from the Tara Oceans dataset and an ocean-biogeochemical model, we demonstrate that ammonium enrichment reduces diatom prevalence in marine ecosystems at the global-scale. Under a high emission scenario, we anticipate 98% of the euphotic zones to experience ammonium enrichment by 2081-2100 and attribute a majority (70%) of future diatom displacement to competitive exclusion by other phytoplankton as bioavailable nitrogen supply shifts from nitrate to ammonium. Overall, the form of nitrogen emerges as a significant but previously underestimated stressor affecting diatoms and ocean ecosystems globally.