These bundled biogeochemical data of sediment core EN20001, from Lake Khamra (59.99095° N, 112.98345° E), in SW Yakutia consist of four datasets: (1) Radiocarbon age dating of bulk sediments from sediment core EN20001 from Lake Khamra, measured at AWI MICADAS; (2) Element composition of the sediment core EN20001 from Lake Khamra, measured at the Bundesanstalt für Geowissenschaften und Rohstoffe (BGR); (3) TOC and TN of the sediment core EN20001 from Lake Khamra, measured in the sediment laboratory at AWI, Potsdam; (4) Pollen and non-pollen palynomorphs of the sediment core EN20001 from Lake Khamra, measured at AWI, Potsdam.This study was additionally supported by a short-term grant (not numbered) from AWI Graduate School (POLMAR), and PhD Completion Scholarship (not numbered) provided by University of Potsdam.