Purpose: The accumulation of trace elements in sediments from highly productive continental margins may depend on the affinity of these elements for organic matter and their degrees of further incorporation into pyrite (FeS2). We tested the hypothesis that the relative contributions of these geochemical phases play a substantial role as trace element (As, Cd, Cr, Cu, Mn, Ni, and Zn) sinks in the highly bioturbated sediments from the tropical upwelling system off Cabo Frio, southeastern Brazil. Materials and methods: Four sediment cores sampled across the Cabo Frio continental shelf were submitted to a sequential extraction procedure performed to separate three different operationally defined fractions, i.e., the geochemical phases soluble in 1 M HCl (considered as the “reactive” fraction), concentrated H2SO4 (considered as the organic matter-bound phase), and concentrated HNO3 (considered as the pyrite-bound phase). The trace metal incorporation into pyrite was assessed by estimating the degree of trace metal pyritization (DTMP), while the pyrite sulfur stable isotope signatures (δ34SPyr) were used as proxies for sulfur redox cycling intensity. Results and discussion: Relative contributions of trace element fixation by organic matter and pyrite were positively correlated for Mn, Cr, and Ni on one hand, and negative correlated for Cu, on the other hand. The positive correlations imply in synergistic roles of these geochemical phases in determining the trace elements sedimentary sinks, while the negative relationship found for Cu reflects differences in the predominant retention mechanisms along with sediment burial. The δ34SPyr signatures were negatively correlated with DTMP values of As, Cd, and Mn, suggesting a diminishing effect of the sulfur redox cycling on trace elements pyritization. These δ34SPyr signatures were not correlated with DTMP values of Cr, Cu, and Ni, which were dominantly associated with the high organic matter contents found in this upwelling system. Conclusions: The role of pelagic organic matter scavenging of metals and later fueling of benthic microbial sulfate reduction and pyrite accumulation were evidenced as highly variable across the Cabo Frio shelf sediments. Differences in the organic matter accumulation in response to upwelling-enhanced primary productivity and in the intensity of bioturbation-driven sulfur redox cycling help to explain the spatial variability in the biogeochemical processes affecting the sedimentary trace metal sinks.