The Jizerka Quaternary alluvial placer in the Czech Republic has been a well-known source of gemstones since the 16th century, and the only one in Europe that has yielded a significant amount of jewel-quality sapphire. Besides Mg-rich ilmenite (“iserine”), which is the most common heavy mineral at the locality, some other minerals have been mined for jewellery purposes. These are corundum (sapphire and ruby varieties), zircon (“hyacinth” gemstone variety) and spinel. Here, we present a detailed petrological and geochronological investigation of the enigmatic relationship between the sapphires and their supposed host rocks, supporting their xenogenetic link. Our hypothesis is based on thermal resetting of the U–Pb isotopic age of the zircon inclusion found inside Jizerka blue sapphire to the estimated time of the anticipated host alkaline basalt intrusion. The host rocks of the gemstones (sapphire and zircon) and Mg-rich ilmenite are not yet known, but could be related to the Cenozoic volcanism located near the Jizerka gem placer (Bukovec diatreme volcano, Pytlácká jáma Pit diatreme and Hruškovy skály basalt pipe). The transport of sapphire, zircon and Mg-rich ilmenite to the surface was connected with serial volcanic events, likely the fast ascent of alkali basalts and formation of multi-explosive diatreme maar structures with later deposition of volcanoclastic material in eluvial and alluvial sediments in nearby areas. All mineral xenocrysts usually show traces of magmatic corrosion textures, indicating disequilibrium with the transporting alkali basalt magma. In order to constrain the provenance and age of the Jizerka placer heavy mineral assemblage, zircon inclusion and associated phases (niobian rutile, baddeleyite and silicate melts) in the blue sapphire have been studied using LA–ICP–MS (laser ablation–inductively coupled plasma–mass spectrometry) geochemistry and U–Pb in situ dating. Modification of the zircon inclusion into baddeleyite by exposure to temperature above 1400 °C in a basaltic melt is accompanied by zircon U–Pb age resetting. A zircon inclusion in a Jizerka sapphire was dated at 31.2 ± 0.4 Ma, and its baddeleyite rim at 31 ± 16 Ma. The composition of the melt inclusions in sapphire and incorporated niobian rutile suggests that the parental rock of the sapphire was alkali syenite. The Eocene to late Miocene (Messinian) ages of Jizerka zircon are new findings within the Eger Graben structure, as well as among the other sapphire–zircon occurrences within the European Variscides. Jizerka blue sapphire mineral inclusions indicate a provenience of this gemstone mineral assemblage from different parental rocks of unknown age and unknown levels of the upper crust or lithospheric mantle.