Perialpine areas of central Europe have undergone significant changes following the last Alpine glaciation and especially through the Holocene time. This study relies on geochronological, mineralogical and geochemical clues to explain the formation and paleoenvironmental significance of FeMn nodules reported from the young soils (~4.5 ka BCE) of Geneva Basin in western Switzerland. Having on average 2 mm in diameter, the nodules usually possess an onion-like and quasi-layered internal architecture defined by selective enrichments in Fe and Mn. Fe-rich mica is largely present in soil matrix and has served as a main source of Fe and Mn. Susceptible to favourable Eh-pH conditions several steps in mica weathering were recognised leading to the formation of nodules – vermiculitization, microcracking, FeMn segregation and re-precipitation. Mineral alterations were boosted by long periods of summer warm climate during Boreal and Atlantic times as suggested by the increasing illite-smectite content and a disappearance of hydroxyl-interlayered clays from analysed colluvium. Moreover, archaeological ages and radiocarbon dating of charcoal yielded coherent FeMn encrustation ages (4.8–4.3 ka BCE and 4.5–4.4 ka BCE, respectively) that coincide with the Holocene temperature maximum (~4 ka BCE) in Central Europe. Terrain morphology that led to better water retention formed earlier than ~8 ka BCE ago, during undefined Late Glacial time, promoting seasonal changes in redox conditions, thus facilitating the mobilization, distribution and re-precipitation of Fe and Mn. Established conditions lasted until Late Neolithic (3.4–2.2 ka BCE) when different agricultural practices changed favourable hydromorphic environment effectively putting an end to further nodule formation.