The most common scientific analysis of archaeological ceramics aims to determine the raw material source and/or production technology. Scientists and archaeologists widely use XRF-based techniques as a tool in a provenance study. After conducting XRF analysis, the results are often analyzed using multivariate analysis in addition to interpretation and conclusions. Various multivariate techniques have already been applied in archaeological ceramics provenance studies to reveal different raw material sources, identify imported pieces, or determine different production recipes. This study aims to evaluate the results of multivariate analysis in the provenance study of ceramics that belong to three cultures that settled in the same area during various prehistoric periods. Portable energy-dispersive X-ray fluorescence spectrometry (pEDXRF) was used to determine the elemental composition of the ceramic material. The ceramic material was prepared in two different ways. The ceramic body material was ground into powder, homogenized, and then pressed into tablets. After that, the same fragments are polished in suitable places. Quantitative and qualitative analyses were performed on the tablets and polished pieces. The results were subjected to both unsupervised and supervised multivariate analysis. Based on the results, it was concluded that qualitative analysis of the well-prepared shards’ surface using EDXRF spectrometry could be utilized in provenance studies, even when the ceramic assemblages were made of similar raw materials.