In this work, the potentialities and limits of the investigation by portable energy-dispersive X-ray fluorescence (XRF) of complex polychrome stratigraphies are discussed. Data are affected by the mutual influence effects of the chemical elements that characterize mineral pigments, by the sequence and the thickness of the paint layers in the stratigraphies and by the size of pigment grains. Sequences of pictorial layers, which produce the typical stratigraphy of cold-painted terracotta and wooden sculptures, have been prepared and then analysed by means of two portable X-ray spectrometers: Innov X Systems Alpha 4000 (Tantalum X-ray tube, 40 kV and 7 µA) and Assing Lithos 3000 (Molybdenum X-ray tube, 25 kV and 300 µA). For each layer of pigment, the XRF spectrum was acquired and the areas of K and L peaks of characterizing elements were calculated. Moreover, the thickness of the layers was determined using XRF data following an algorithm already shown and the values have been compared with those measured on polished cross sections observed by optical microscope in reflected light.