Impurities in paint layers executed with green and blue copper pigments, although relatively common, have been studied only little to date. Yet, their proper identification is a powerful tool for classification of paintings, and, potentially, for future provenance studies. In this paper, we present analyses of copper pigments layers from wall paintings situated in the vicinity of copper ore deposits (the palace in Kielce, the palace in Ciechanowice, and the parish church in Chotków) located within the contemporary borders of Poland. We compare the results with the analyses of copper minerals from three deposits, two local, and one historically important for the supply of copper in Europe, i.e., Miedzianka in the Holy Cross Mountains, Miedzianka in the Sudetes, and, as a reference, Špania Dolina in the Slovakian Low Tatra. Optical (OM) and electron microscopy (SEM-EDS), Raman spectroscopy, and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have been used for a detailed investigation of the minute grains. Special attention has been devoted to antimony and nickel phases, as more unusual than the commonly described iron oxides. Analyses of minerals from the deposits helped to interpret the results obtained from the paint samples. For the first time, quantitative analyses of copper pigments’ impurities have been described.