This paper reports the first-ever study on nanoscale mineralogy in pyrite from the volcanogenic massive sulfide (VMS) deposits of the Iberian Pyrite Belt, southwestern Iberian Peninsula. It targeted colloform-textured grains formed at low temperature in the distal part of a polymetallic (Pb-Zn) massive sulfide lens hosted in felsic volcanoclastic rocks from the Masa Valverde deposit, and euhedral-textured grains (re)-deposited by higher temperature fluids in the Co-Au rich stockwork hosted in black shales of the Filón Norte orebody of the Tharsis deposit. The results acquired by a combination of techniques for mineral microanalysis and characterization (i.e., reflected light, FE-SEM, EPMA, LA-ICP-MS, HRTEM-STEM and TEM-EDS) show that trace amounts of metals (Au, Ag, As, Pb, Sb, Cu, Co) are incorporated as both lattice-bound and into nanoparticles (NPs). The mode of occurrence is strongly related with the evolutionary history of the mineralization. In the colloform pyrite collected from the massive sulfide lens, a rhythmic banding/oscillatory zonation with up to 3 wt% As, 5,000 ppm Pb, 1,070 ppm Sb and 750 ppm Cu is defined by the coexistence of several nano-sized layers (5 to 100 nm) and NPs (<100 nm) containing all these metals. The NPs include galena [PbS], tetrahedrite [(Cu,Fe)12Sb4S13)] and arsenopyrite [FeAsS] that exhibit euhedral and less frequently anhedral (i.e., droplet-like) morphologies being both randomly and preferentially oriented with respect to As-rich pyrite bands they are usually associated with. These features suggest formation of the NPs via direct deposition from the hydrothermal fluid(s) or low-temperature melts entrained in them as well as exsolution of trace elements originally dissolved in the As-rich pyrite structure. Additionally, some of these NPs are connected to late fractures disrupting the chemical zoning in colloform pyrite documenting a third genetic type of NPs related to late infiltration of fluids post-dating pyrite formation. In contrast, euhedral pyrite from the stockwork form well-developed homogeneous grains with discrete porous areas relatively depleted in Fe (45.20 wt%), and As (8,800 ppm) but enriched in Co (5,900 ppm). At the nanoscale, Co-enriched domains show patchy zoning defined by irregular distribution of Co– and As-rich bands of 200–500 nm in thickness. These nanometer Co– and As-rich bands are often disrupted by micron-to-nano-sized polycrystalline Au-Ag-Hg particles that fill voids in porous areas. Contact morphology anatomy between Co-rich pyrite and inclusions suggests that the Au-Ag-Hg particles are negative crystals occupying spaces originated in pyrite by coupled dissolution-reprecipitation reaction. Likewise, HRTEM observations along such pyrite-inclusion contacts show the existence of polycrystalline matrices in both pyrite and Au-Ag-Hg inclusions, the former consisting of nano-sized domains of arsenian pyrite and/or arsenopyrite in As-free pyrite and the Au-Ag-Hg inclusions made up of multiple crystal domains including nano-crystallites of Au0/Ag0 or electrum. Recognition of crystalline nanodomains and NPs in these polycrystalline matrices raises the possibility that Au NPs or nanomelts already present in the hydrothermal fluid catalyzed the formation of these heterogeneous crystals.