The Vathi porphyry Cu-Au±Mo deposit is located in the Kilkis ore district, northern Greece. Hydrothermally altered and mineralized samples of latite and quartz monzonite are enriched with numerous rare and critical metals. The present study focuses on the bulk geochemistry and the mineral chemistry of pyrite, chalcopyrite, magnetite, and titanite. Pyrite and chalcopyrite are the most abundant ore minerals at Vathi and are related to potassic, propylitic, and sericitic hydrothermal alterations (A- and D-veins), as well as to the late-stage epithermal overprint (E-veins). Magnetite and titanite are found mainly in M-type veins and as disseminations in the potassic-calcic alteration of quartz monzonite. Disseminated magnetite is also present in the potassic alteration in latite, which is overprinted by sericitic alteration. Scanning electron microscopy and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analyses of pyrite and chalcopyrite reveal the presence of pyrrhotite, galena, and Bi-telluride inclusions in pyrite and enrichments of Ag, Co, Sb, Se, and Ti. Chalcopyrite hosts bornite, sphalerite, galena, and Bi-sulfosalt inclusions and is enriched with Ag, In, and Ti. Inclusions of wittichenite, tetradymite, and cuprobismutite reflect enrichments of Te and Bi in the mineralizing fluids. Native gold is related to A- and D-type veins and is found as nano-inclusions in pyrite. Titanite inclusions characterize magnetite, whereas titanite is a major host of Ce, Gd, La, Nd, Sm, Th, and W.