In this study, a multidisciplinary approach was used for a detailed characterization of sediments from the archaeological site Vinča – Belo Brdo, Serbia, one of the most important Neolithic settlements in Europe. This research aimed to determine the paleoenvironmental conditions during Pleistocene and Early Holocene sedimentation prior to Early Neolithic settlement (~5800 cal BC) and provide novel insight into the interaction between humans and the environment during the Middle and Late Neolithic (5300–4550 cal BC). For the first time, organic geochemical characterization, combined with organic petrography, grain size, mineralogy, and inorganic analysis were done on sediment samples from geological and archaeological sections of the Vinča – Belo Brdo site. In the archaeological section, the layer with remains of the burned house and the overlaying leveling layer were particularly interesting.The samples from the oldest geological layers were characterized by the relatively high content of carbonates, the largest amount of soluble organic matter (OM), predominance of liptinite macerals, along with the prevalence of short and mid-chain n-alkanes indicating a marsh-lake depositional environment. The sedimentation of overlaying geological layers continued in an oxbow lake, followed by a shallow depositional environment with stronger input of vascular plants. This was indicated by an increase of the terrigenous component, a high amount of huminite maceral, especially textinite, the predominance of odd long-chain n-alkanes, as well as the presence of diterpanes, pimarane, and 16α(H)-phyllocladane.Quartz was the most abundant mineral in paleosol, while the OM had a mixed origin with a major input of microorganism in the precursor biomass. Estimated average paleosol temperature around 12–16 °C and mean annual precipitation of 938 mm/yr were favorable for ancient civilization settlement.In archaeological samples, the OM was predominantly formed by microorganisms, with a certain contribution of terrestrial plants. Their occurrence was substantiated by the presence of telohuminite, detrohuminite, resinite, and sporinite. The prevalence of n-alkane C18, along with the occurrence of inertinite macerals, semifusinite and fusinite, in the layer with the burned house remains confirmed the incomplete combustion of woody biomass at temperatures <500 °C. Organic and inorganic geochemical parameters for the leveling layer covering the destroyed buildings showed analogous composition as the lowest geological layers. This proved that Vinča inhabitants excavated material for leveling at a site in their vicinity, and used it for covering the burnt debris, clearing the areas for a new settlement. In this context, the decades long archaeological dilemma of the origin of the leveling material was resolved.