The Indian Ocean accounts for about one fifth of global ocean net primary production but remains undersampled relative to other major ocean basins. The eastern tropical Indian Ocean is characterized by extremely low concentrations of both macronutrients and the micronutrient iron. We measured concentrations of dissolved and particulate trace metals (Fe, Mn, Zn, Pb) in the upper ocean along the GO-SHIP IO9N transect (28˚S to 17˚N, mostly along the 95˚E meridian) during a cruise in April 2016. Cellular quotas (metal/C) of Fe, Mn, Co, Ni, Cu, and Zn were measured in small eukaryotic flagellates (2–7 μm). Deckboard bottle incubation experiments were conducted at one station in each of three putative biogeochemical regions: southern Indian Ocean gyre (SIO, 28-10˚S); equatorial Indian Ocean (EqIO, 10˚S - 5˚N); Bay of Bengal (BoB, 5-17˚N). Nitrate and phosphate were below detection limits in surface waters across the transect. Dissolved and particulate Fe were <0.2 nM south of 10˚N and lowest in the EqIO. Cellular Fe/C quotas were approximately 6 μmoL/mol and did not vary along the transect, nor did cellular Mn/C or Co/C quotas. Cellular Ni/C and Zn/C quotas were significantly higher at the southern terminus. Nutrient addition experiments indicated that N was the primary limiting nutrient for autotrophs using chlorophyll a as a proxy, but biomass measurements of specific phytoplankton groups pointed to a more complex nutrient limitation mosaic. Prochlorococcus was limited by N in the EqIO but by multiple nutrients (N, P, and/or Fe) in the BoB. Synechococcus was limited by N in the EqIO and BoB, while small (<20 μm) eukaryotic phytoplankton were limited by N in the EqIO and by multiple nutrients in the BoB. Stoichiometric comparisons of cells and underlying source waters indicate a gradient of N and Fe stress along the transect. These data demonstrate that autotroph communities are poised near multiple nutrient limitation horizons in extremely oligotrophic waters far from micronutrient sources.