The Konos Hill and Pagoni Rachi porphyry-epithermal prospects in northeastern Greece are characterized by abundant pyrite that displays important textural and geochemical variations between the various ore stages. It is commonly fine-grained and anhedral in the porphyry-related mineralization (M- and D-type veins), while it forms idiomorphic, medium- to coarse-grained crystals in the late, epithermal style veins (E-type). Porphyry-style pyrite from both prospects is characterized by an enrichment in Co, Se, Cu, and minor Zn, and a depletion in other trace elements, like Bi, Mo, Ag, etc. Pyrite in epithermal-style mineralization is mostly characterized by the presence of As, Bi, Pb, Ni, and Se. Gold in pyrite from all mineralization stages occurs as a non-stoichiometric substituting element, and its abundance correlates with As content. Arsenic in pyrite from Konos Hill records an increase from the porphyry stage to the epithermal stage (along with gold); however, at Pagoni Rachi, the highest Au and As contents are recorded in D-type pyrite and in the epithermal stage. The composition of the studied pyrite marks changes in the physico-chemical conditions of the ore-forming fluids and generally follows the geochemical trends from other porphyry-epithermal systems elsewhere. However, a notable enrichment of Se in the porphyry-style pyrite here is a prominent feature compared to other deposits and can be considered as an exploration tool towards Au-enriched mineralized areas.