Phytoplankton, the dominant primary producers in the global ocean, are essential to oceanic nutrient cycling but the impact of climate change on the interactions between phytoplankton and biogeochemical cycles are uncertain. As for all biological material, phytoplankton require an array of macronutrient elements, such as C, N, P, and S, and an extended suite of trace metal micronutrients required as cofactors/coenzymes that regulate essential photosynthetic and metabolic pathways, including Fe, Zn, Mn, Ni, Cu, Co, Se, and Mo. Trace metal cellular inventories, or quotas, have been shown to vary over orders of magnitude both between key taxa, and within taxonomic groups between ocean basins and across biogeochemical gradients, but the methodologies used to date are hampered by throughput. Here we apply a high-throughput correlative multimodal imaging pipeline to quantify single cell element quotas of natural marine phytoplankton using laser ablation-inductively coupled plasma-time of flight mass spectrometry (LA-ICP-TOFMS). Surface samples were taken along meridional transects in the E. Pacific and E. Atlantic sub-Antarctic zones of the Southern Ocean. These transects encompassed strong biogeochemical gradients (NO₃^- 25 to 0.0µM, PO₄^3- 1.7 to 0.1µM, SiO₂ 61 to 0.7µM, SST 0.3 to 24.2^oC, Chl-a 3.2 to 0.06µg/L), including transitions from Fe-limited Southern Ocean waters to N-limited subtropical regimes, as well as regions of Fe–Mn co-limitation associated with major productivity along the Polar Front. Resolving the variability in trace metal single cell stoichiometry within natural phytoplankton assemblages over greater spatial and temporal scales is crucial to better model primary production and biogeochemical cycling into the future under different climate forcing scenarios.