Ecuadorian pottery is renowned for its beauty and the particularly rich colour of its pigments. However, a major challenge for art historians is the proper assessment of the provenance of individual pieces due to their lack of archaeological context. Of particular interest is the Jama-Coaque culture, which produced fascinating anthropomorphic and zoomorphic pottery from ca. 240 B.C. until the Spanish Conquest of 1532 A.D. in the coastal region of Ecuador. Using a combination of microscopic and spectroscopic techniques, i.e., transmission electron microscopy (TEM), Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive x-ray spectroscopy (EDX), and scanning electron microscopy (SEM); we are able to characterize these pieces. We have found several kinds of iron-oxide based nanostructures in all the colour pigments we investigated for the Jama-Coaque culture, suggesting the same unique volcanic source material was used for their clay. Such nanostructures were absent from the pigment samples studied from other contemporary coastal-Ecuadorian cultures, i.e., the Tumaco-La Tolita and Bahía cultures. In the yellow pigments of goethite we find carbon nanofibres, indicating these pigments were subjected to a thermal treatment. Finally, in the blue, green, and black pigments we detect modern pigments (phthalocyanine blue, lithopone, and titanium white), suggesting modern restoration. Our results demonstrate the power of TEM, Raman, FTIR, EDX, and SEM archaeometric techniques for characterizing pieces without a clear archaeological context. Furthermore, the characterization of nanostructures present in such pieces could be used as a possible fingerprint for a provenance study.