A number of ecological and geochemical transformations occurred during late Ediacaran and early Cambrian time, the effects of which are difficult to overestimate. However, the strong linkage of biostratigraphic and chemostratigraphic methods with lithofacies makes the localization of the Precambrian–Cambrian boundary and its correlation with lithologically contrasting sections highly debatable. We analyse the taxonomy and stratigraphic distribution of small skeletal fossils and trace fossils, the carbonate carbon and oxygen isotope composition, and U–Pb detrital zircon age in the Ediacaran–Cambrian transitional interval of the Irkutsk Cis–Sayans Uplift (southwestern Siberian Platform). This interval (Moty Group) comprises a transgressive succession with red-coloured alluvial to deltaic siliciclastic deposits (Shaman Formation) and overlying shallow-marine carbonates (Irkut Formation). The lower Irkut Formation hosts sporadic and poorly preserved tubular Cambrotubulus fossils, which are known from both the terminal Ediacaran Period (c. 550–541 Ma) and the Terreneuvian Epoch (541–521 Ma), and typical Fortunian trace fossils, including an index ichnotaxon of the Cambrian boundary Treptichnus pedum. The biostratigraphic and carbonate carbon isotope data and U–Pb concordia ages of 531.1 ± 5.2 Ma (mean weighted, 530.6 ± 5.3 Ma) of the five youngest zircon grains from the lower Irkut Formation indicate that at least the shallow-marine carbonates of the upper Moty Group correspond to the Cambrian Stage 2 (c. 529–521 Ma). In the Irkutsk Cis–Sayans Uplift, the Cambrian Period tentatively began before or during the accumulation of the alluvial to deltaic siliciclastic Khuzhir and Shaman formations, and this crucial divide remained unmarked in the palaeontological and isotopic records.