This article presents the use of Raman spectroscopy to test the composition of paint detected in petroglyphs on old red sandstone in the Minusinsk Basin. Because this sandstone is saturated with iron compounds, it is extremely difficult to distinguish components of red paint based on mineral raw materials from those of the rock surface. We elaborated a two-stage technique. First, the composition of the rock surface was analyzed using Raman spectroscopy. Second, the concentration of substances on the surface was assessed using indexes of relative peak intensity in the spectra using statistical methods (Mann-Whitney U-test, principal component analysis). The procedure was tested at three rock art sites in the Minusinsk Basin. The examination of panel 15 at Tepsei I (Krasnoturansky District, Krasnoyarsk Territory) suggests that when the rock is heavily damaged by environmental processes such as ferruginization, oxalate accretions, oxidation and weathering products, the composition of the paint is indistinguishable from that of the substrate. At Oglakhty IV (Bogradsky District, Republic of Khakassia), analysis revealed that local mineral raw materials from metamorphosed sandstone subjected to heat treatment were used. On panels 7–9 in section 1A of Shalabolino (Kuraginsky District, Krasnoyarsk Territory), two paints were used. The lighter color was made of ocher, the outcrops of which in the form of metamorphosed sandstone were found within the boundaries of the site. The darker paint was made from apatite-magnetite ore. In both cases, the mineral raw materials were subjected to heating. This method will be used to study a larger sample of rock art paintings in the Minusinsk Basin.