Trace element compositions of magnetite and hematite from 16 well-studied iron oxide–copper–gold (IOCG) and iron oxide apatite (IOA) deposits, combined with partial least squares-discriminant analysis (PLS-DA), were used to investigate the factors controlling the iron oxide chemistry and the links between the chemical composition of iron oxides and hydrothermal processes, as divided by alteration types and IOCG and IOA deposit subtypes. Chemical compositions of iron oxides are controlled by oxygen fugacity, temperature, co-precipitating sulfides, and host rocks. Iron oxides from hematite IOCG deposits show relatively high Nb, Cu, Mo, W, and Sn contents, and can be discriminated from those from magnetite + hematite and magnetite IOA deposits. Magnetite IOCG deposits show a compositional diversity and overlap with the three other types, which may be due to the incremental development of high-temperature Ca–Fe and K–Fe alteration. Iron oxides from the high-temperature Ca–Fe alteration can be discriminated from those from high- and low-temperature K–Fe alteration by higher Mg and V contents. Iron oxides from low-temperature K–Fe alteration can be discriminated from those from high-temperature K–Fe alteration by higher Si, Ca, Zr, W, Nb, and Mo contents. Iron oxides from IOA deposits can be discriminated from those from IOCG deposits by higher Mg, Ti, V, Pb, and Sc contents. The composition of IOCG and IOA iron oxides can be discriminated from those from porphyry Cu, Ni–Cu, and volcanogenic massive sulfide deposits.