Magnetite is a widespread mineral, as disseminated or massive ore. Representative magnetite samples separated from various geotectonic settings and rock-types, such as calc-alkaline and ophiolitic rocks, porphyry-Cu deposit, skarn-type, ultramafic lavas, black coastal sands, and metamorphosed Fe–Ni-laterites deposits, were investigated using SEM/EDS and ICP-MS analysis. The aim of this study was to establish potential relationships between composition, physico/chemical conditions, magnetite origin, and exploration for ore deposits. Trace elements, hosted either in the magnetite structure or as inclusions and co-existing mineral, revealed differences between magnetite separates of magmatic and hydrothermal origin, and hydrothermal magnetite separates associated with calc-alkaline rocks and ophiolites. First data on magnetite separates from coastal sands of Kos Island indicate elevated rare earth elements (REEs), Ti, and V contents, linked probably back to an andesitic volcanic source, while magnetite separated from metamorphosed small Fe–Ni-laterites occurrences is REE-depleted compared to large laterite deposits. Although porphyry-Cu deposits have a common origin in a supra-subduction environment, platinum-group elements (PGEs) have not been found in many porphyry-Cu deposits. The trace element content and the presence of abundant magnetite separates provide valuable evidence for discrimination between porphyry-Cu–Au–Pd–Pt and those lacking precious metals. Thus, despite the potential re-distribution of trace elements, including REE and PGE in magnetite-bearing deposits, they may provide valuable evidence for their origin and exploration.