The supply of limiting nutrients to the low latitude ocean is controlled by physical processes linked to climate variations, but methods for reconstructing past nutrient concentrations in the surface ocean are few and indirect. Here, we present laser ablation mass spectrometry results that reveal annual cycles of P/Ca in a 4-year record from the scleractinian coral Pavona gigantea (mean P/Ca = 118 μmol mol−1). The P/Ca cycles track variations in past seawater phosphate concentration synchronously with skeletal Sr/Ca-derived temperature variations associated with seasonal upwelling in the Gulf of Panamá. Skeletal P/Ca varies seasonally by 2–3 fold, reflecting the timing and magnitude of dissolved phosphate variations. Solution cleaning experiments on drilled coral powders show that over 60% of skeletal P occurs in intracrystalline organic phases. Coral skeleton P/Ca holds promise as a proxy record of nutrient availability on time scales of decades to millennia.