• High spatial-resolution techniques allowed the study of complex layered structures. • We characterised carnation and red colours in Romanesque mural paintings. • Visual inspection and material composition analysis match old treatises instructions. • We detected eight different pigments according Theophilus' and Hermeneia treatises. • We verified the use of the three-tone procedure in Sant Climent de Taüll paintings. Medieval texts describe the use of the three-tone system as a pictorial procedure characteristic of Romanesque art to represent shape and volume. Some Medieval art treatises provide detailed instructions of its application, using specific names for each of the carnation colours: membran a (mid-tone or base colour), rosa and posc (darker) and lumen (lighter). In this study we have verified its use and application by analysing the mural paintings of the central apse of the church of Sant Climent de Taüll (Catalonia), currently on display at the Museu Nacional d'Art de Catalunya. A combination of microanalytical techniques, micro-infrared spectroscopy (μFTIR), synchrotron-based micro-X-ray diffraction (µSR-XRD), Scanning Electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and Optical microscopy (OM), provided precise information on the composition and distribution of the compounds in the sequence of micrometric layers. We have identified the use of up to eight different pigments carefully mixed, to obtain a variety of tones in accordance to the recipes given in the Theophilus' De diversis Artibus and the Hermeneia (Byzantine pictorial tradition). The inner layers, painted directly on the still wet lime mortar, show the typical carbonation microstructure of fresco , while the surface layers for the contours of geometric decorative elements and figures which required longer working times, were applied al secco. [Display omitted] [ABSTRACT FROM AUTHOR]