A geochemical and mineralogical approach was used to analyze 3rd millennium BCE pottery from Southeast Lithuania that is attributed to the foreign Corded Ware Culture and local hunter-gatherers. SEM-EDS, XRF, XRD, and FTIR were used to study the peculiarities of the pottery and to develop hypotheses about the raw material and technology choices present. The amounts of ten major elements in the bulk and clay matrix compositions (XRF, SEM-EDS) and eleven trace analytes in the bulk compositions (XRF) were compared with the Clarke values and tested to highlight the significance (Mann–Whitney U and Wilcoxon Matched Pairs Tests) of the differences in the elemental quantities between the clay matrix and bulk compositions, and between the lighter and darker clay matrixes. These also revealed the advantage of Ward’s clustering method using the City-block distance of bulk compositions as a tool for inter-correlating ceramics in attributing them to specific communities and locations. The XRD, FTIR, and SEM-EDS mineralogical analyses indicated a predominance of iron-rich illite clay, quartz, and alkali feldspar, in addition to very low to medium firing temperatures. All of the pottery samples consisted of hydromicaceous clay from local Quaternary glacial sediments that contain weathered granitoid fragments.