The East Australian Current (EAC) system is characterized by a dynamic eddy field that modulates nutrient availability and therefore phytoplankton growth. Eddies can stimulate or suppress productivity through a number of bio-physical mechanisms. We examine remote sensing and in-situ profile data over 20 years (2003 to 2022) to disentangle the influence of EAC eddies on seasonal cycles of biogeochemical anomalies. First, we analyze the anomalies of phytoplankton biomass observed by satellites. The eddy-induced anomalies differ in the polarity of eddies and show a seasonal pattern, but the polarity dependence and seasonal patterns vary with latitude (from north to south). Next, we construct composite cyclones and anticyclones from BGC-Argo profiles over the same time period to understand the three-dimensional structure of biogeochemical anomalies. The physical anomalies comply with the classical view of eddy dynamics, but the biogeochemical anomalies show a more complex pattern in the eddies. This is the first systematic examination of the depth-resolved structure of biogeochemical anomalies inside EAC eddies. These results will help us improve the quantification of biogeochemical cycles in the EAC system, constraining future projections of primary productivity in the EAC region.