The Yana–Kolyma metallogenic belt, NE Russia, is a world-class gold belt with resources numbering ~8300 tons of gold. The belt is localized in the central part of the Verkhoyansk–Kolyma orogen, formed by a collage of diverse terranes. The Tithonian-to-Early-Cretaceous orogenic gold deposits are hosted in a sequence of Permian–Triassic and Jurassic clastic rocks and altered Late Jurassic andesite, dacite, granodiorite, trachyandesite, and trachybasalt dykes. High-fineness gold (800–900‰) in quartz veins and invisible gold in disseminated arsenian pyrite-3 (Py3) and arsenopyrite-1 (Apy1) are present in ores. Here, we present new data about microtextures; the chemical composition and stable sulfur isotopes of auriferous pyrite-3 and arsenopyrite-1 from proximal alterations in sediment-hosted (Malo–Taryn, Badran, Khangalas); and intrusion-hosted (V’yun, Shumniy) orogenic Au deposits in the central sector of the Yana–Kolyma metallogenic belt to better constrain the ore-forming process and tracking their evolution. Detailed petrography defined the following generations of pyrite: syn-sedimentary/diagenetic Py1, metamorphic Py2 and hydrothermal Py3, and Apy1. Hydrothermal Py3 and Apy1 are localized in the proximal pyrite–arsenopyrite–sericite–carbonate–quartz alteration in ore zones and make a major contribution to the economic value of the veinlet-disseminated mineralization with “invisible” gold in the orogenic deposits of the Yana–Kolyma metallogenic belt. Electron microprobe analysis (EMPA) of Py3 in both types of deposits shows concentrations of As (up to 3.16 wt%), Co, Ni, Cu, Sb, and Pb. Py3 in intrusion-hosted orogenic gold deposits reveals elevated concentrations of Co (up to 0.87 wt%), Ni (up to 3.52 wt%), and Cu (up to 2.31 wt%). The identified negative correlation between S and As indicates an isomorphic substitution of sulfur by As1−. Py3 from igneous rocks is characterized by a high degree of correlation for the pairs Fe2+→ Co2+ and Fe2+→ Ni2+. For hydrothermal Apy1, Co (up to 0.27 wt%), Ni (up to 0.30 wt%), Cu (up to 0.04 wt%), and Sb (up to 0.76 wt%) are typomorphic. According to atomic absorption spectrometry, the concentration of Au in Py3 reaches 159.5 ppm; in Apy1, it reaches 168.5 ppm. The determination of the precise site of the invisible gold within Py3 and Apy1 showed the predominance of solid-solution Au+ in the crystal lattice. The values of δ34S in Py3 and Apy1 (from −6.4 to +5.6‰, mean value of about +0.6‰), both from sediment-hosted and from intrusion-hosted deposits, display a relatively narrow range and are characteristic of the hydrothermal ore stage. Our analytical results showed no systematic differences between the chemical and stable sulfur isotope compositions of both auriferous pyrite-3 and arsenopyrite-1 from the proximal alteration in sediment-hosted (Malo–Taryn, Badran, Khangalas) and intrusion-hosted (V’yun, Shumniy) orogenic Au deposits, indicating that the primary source of sulfur, gold, and mineralizing fluids was likely from subcrustal and metamorphic systems in the Late-Jurassic-to-Early-Cretaceous Verkhoyansk–Kolyma orogen.