Although Scandinavian flint is one of the most important materials used for prehistoric stone tool production in Northern and Central Europe, a conclusive method for securely differentiating between flint sources, geologically bound to northern European chalk formations, has never been achieved. The main problems with traditional approaches concern the oftentimes high similarities of SiO2 raw materials (i.e. chert and flint) on different scales due to similar genetic conditions and higher intra- than inter-source variation. Conventional chert and flint provenance studies chiefly concentrate on visual, petrographic or geochemical investigations. Hence, attempts to generate characteristic fingerprints of particular chert raw materials were in most cases unsatisfying. Here we show that the Multi Layered Chert Sourcing Approach (MLA) achieves a clear differentiation between primary sources of Scandinavian flint. The MLA combines visual comparative studies, stereo-microscopic analyses of microfossil inclusions, geochemical trace element analyses applying LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry) and statistical analyses through CODA (Compositional Data Analysis). For archaeologists, provenance studies are the gateway to advance interpretations of economic behavior expressed in resource management strategies entailing the procurement, use and distribution of lithic raw materials. We demonstrate the relevance of our results for archaeological materials in a case study in which we were able to differentiate between Scandinavian flint sources and establish the provenance of historic ballast flint from a shipwreck found near Kristiansand close to the shore of southern Norway from a beach source in Northern Jutland, the Vigsø Bay.