The Jaguar nickel deposit represents an important and unconventional discovery of hydrothermal Ni resources (58.9 Mt @ 0.95% Ni) associated with magnetite and apatite within the Carajás Mineral Province, Northern Brazil. The Jaguar deposit shares several similarities with iron oxide copper–gold (IOCG) deposits of the Carajás Mineral Province, especially regarding the structural control, and the hydrothermal alteration. Although IOCG and Kiruna-type iron oxide-apatite (IOA) deposits are closely associated in several geological provinces, this association has not yet been fully constrained in the Carajás Mineral Province. The Jaguar deposit occurs near mafic–ultramafic intrusions, along a regional fault zone, and is hosted either by granitic (northern portion) or felsic subvolcanic (southern portion) rocks. It is characterized by sub-vertical zones hosting a biotite-chlorite (Bt-Chl) hydrothermal alteration with ductile structures and disseminated sulfides (pyrite and millerite) and magnetite. These zones are overprinted by sulfide-magnetite-apatite-bearing breccias, which represent the main mineralization bodies. The sulfide assemblage in the mineralized zones is dominated by pyrite, pentlandite and millerite, with minor sphalerite and chalcopyrite.We have investigated the concentration of trace elements in the magnetite and sulfides from the host rocks, different alteration facies and the mineralization at the Jaguar deposit by LA-ICP-MS. Magnetite composition ranges from higher Al, Mn, Ti and V contents, for at least part of those in host rocks (granitic and felsic subvolcanic) and Bt-Chl alteration, into lower contents in the magnetite-apatite alteration, associated with the main Ni mineralization. Magnetite with higher Ti and V contents in host rocks is associated with discrete hydrothermal alteration pockets, have high Ni/Cr ratios and plot in high temperature hydrothermal fields in multi-element diagrams. Therefore, we support that these features are compatible with a hydrothermal origin. Anomalously high-Ni contents in magnetite point that the Neoarchean mafic–ultramafic layered intrusions of the Carajás Province represent potential Ni sources for hydrothermal remobilization. Anomalously high V contents in magnetite suggest lower fO2 conditions upon the formation of the deposit. The concentration of trace elements in magnetite associated with the Jaguar deposit is similar to those from other IOCG deposits from the Carajás Province (but with higher V and Ni contents), especially the Sossego mine in the Southern Copper Belt, indicating that it could represent a Ni-rich member of the regional-scale IOCG mineral system at Carajás. Pyrite and chalcopyrite have a composition similar to those from magmatic deposits, when using previously proposed discriminant diagrams, but this is also the case for other IOA and IOCG deposits. However, low PGE contents (Ru, Rh, Ir and Os) in pyrite from the Jaguar deposit support a hydrothermal origin. Our results highlight that the classifications provided by available discriminant diagrams are not unequivocal. We suggest that multi-element diagrams represent a complementary approach to binary plots and provide a more comprehensive classification for the use of indicator minerals.