Two precious Carolingian manuscripts kept in the library of Kremsmuenster Abbey in Upper Austria were subject of investigation. The well-known Codices Millenarius Maior (Inv. No. CC Cim 1, Fig. 1a) and Millenarius Minor (Inv. No. CC Cim 2, Fig. 1b) were studied within the framework of the Centre of Image and Material Analysis in Cultural Heritage (CIMA) in Vienna. The manuscripts are especially famous for their precious and colorful miniatures of a very early medieval period. The aim of the work was the material identification (colors and inks) used for the make-up of the two codices in order to gain a better understanding of their evolution and their provenance. The instrumentation available in the CIMA laboratories allowed performing in situ measurements using non-destructive and non-invasive analytical methods. The investigations comprised a combination of three complementary methods: X-ray fluorescence analysis (XRF), Fourier transform infrared spectrometry in the reflection mode (rFTIR) and Raman spectrometry. In addition to the identification of the pigments and inks also a detailed characterization of the parchment concerning its manufacturing process was achieved by that combination. The identification of calcium carbonates on the surface of the parchment is an indicator for the liming or whitening of the animal skin, whereas the polishing process of the parchment surface with pumice stone, left traces of silicates, detected by rFTIR. The combination of XRF and Raman spectrometry enabled the characterization of black/brown inks in the text revealing the usage of iron gall inks. For the red inks applied for text and initials vermilion and red lead were applied in both codices. Furthermore, the pigment palette used for the illumination included: lead white, orpiment/realgar, red lead, vermilion and red iron oxides as well as azurite and indigo, together with the rather rare copper chloride hydroxide. Furthermore, in both gospels the application of metal leaves as well as powders made of silver–copper and gold–copper alloys could be determined by XRF on several folios.