The yellow coloring of the organic and inorganic pigments used in large Buddhist paintings during the late Joseon dynasty (17th–19th centuries) is herein analyzed using Raman spectroscopy and non-invasive component analysis via p-XRF. p-XRF analyses of 194 yellow points on 12 large Buddhist paintings confirmed the use of gold, orpiment, and organic pigments; however, the yellow chromophoric elements of the organic pigments were not detected. The confirmed colors ranged from light yellow (close to white) to bright and dark yellow, but microscopic analysis revealed no particles or crystals. Accurate identification of pigments comprising light elements or organic compounds is challenging, which limits their identification via p-XRF. In contrast, Raman spectroscopy of the samples presumed to be organic pigments detected gamboge in the samples, either alone, mixed with a white inorganic pigment such as lead white to express yellow, or overlaid upon such a pigment. These results demonstrate the utility of Raman spectroscopy in the analysis of organic pigments and provide a guide for the identification of coloring materials used in cultural heritage artifacts.