The Čoka Marin polymetallic (Cu-Au-Ag-Zn-Pb) deposit belongs to the world-class Bor ore district in Serbia and consists of three lens-shaped orebodies hosted by Late Cretaceous andesitic volcanic rocks. Pyrite is the dominant mineral in the deposit and shows a great variety of textures and zoning. It occurs as fine- to coarse-grained crystals and massive, spongy, colloform, framboidal, oolitic, and replacement aggregates. Complex relationships with other minerals and the presence of microscale mineral inclusions and micro- to nanoscale porosity are common features of the pyrite at Čoka Marin. Minor amounts of Cu (up to 7.9 wt.%), Pb (up to 7 wt.%), As (up to 4 wt.%), Ag (up to 1 wt.%), Te (up to 0.07 wt.%), and rarely Sb (up to 0.11 wt.%) were detected in pyrite using an electron microprobe. Zoning and heterogeneity in pyrite is mainly caused by variable copper content. Structurally bound Cu in pyrite from this deposit reported in a previous study was confirmed by our new electron microprobe analyses. Distinct Pb-bearing zones frequently occur in pyrite following oscillatory zoning and crystal shapes. These zones also contain lesser amounts of the other elements mentioned above. Using the focused ion beam (FIB) technique to prepare electron-transparent foils and transmission electron microscopy (TEM), we found that these elements form nanoscale Pb-(±As, Ag, Cu)-bearing inclusions (mosty <50 nm) in these distinct zones. Sector zoning in pyrite is caused by the presence of Ag and Pb and is evidence for a purely crystallographic control of a nanoscale inclusion entrapment during pyrite growth. Entrapment of nanoscale Pb-bearing inclusions in distinct crystal zones of pyrite, as well as complex mineral relationships in the deposit, were most likely associated with abrupt changes in ore-forming conditions and rapid co-precipitation of metal sulfides in a sub-volcanic environment. This study reports the first evidence of Pb-bearing pyrite zones containing nanoscale inclusions and shows a good example of the use of FIB-TEM techniques in resolving the dilemma of whether chemical impurities form solid solutions or nanoscale inclusions in a mineral.