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Scientific interest in analytical tools that enable reliable, repeatable, and rapid measurements without sampling is growing in the field of cultural heritage. Therefore, improving the use of methods that permit an efficient characterization of a wide range of materials through non-invasive and portable instruments, such as spectroscopies, is currently in high demand. This work is focused on the non-invasive study and identification of selected red and yellow pigments containing oxides and sulfides, frequently used in ancient wall-paintings, by means of portable External Reflectance Fourier Transform Infrared spectroscopy (ER-FTIR) within an extended spectral range (7500 - 360 cm−1) which includes a portion of far IR addressing diagnostic peaks and band assignment for the first time. In this work we have also examined the reflection signals of the pigments when applied on a surface representing a fresco wall-painting, to discuss possible changes of the profile as the optical and morphological properties of the surface change. For this purpose, yellow and red oxides, ochres, Siennas, minium, orpiment, and vermillion were selected and used to produce laboratory mock-ups of fresco paints. The ER-FTIR signals obtained on raw pigments were firstly validated by portable non-invasive Raman spectroscopy and X-Ray Fluorescence, and bench-top X-Ray powder Diffraction. Then, the results were subsequently compared with the ER-FTIR signals collected on the mock-ups to discuss the changes in the reflection spectral profile when in presence of rough surfaces and matrix-effects. The combined study on reference materials and mock-ups allowed to identify and discuss ER-FTIR marker bands which were finally validated on real samples of three fragments of Roman frescos provided by the Archeological Museum “San Lorenzo” in Cremona. The proposed method demonstrates distinctive IR features from external reflection analysis on the selected pigments, scarcely studied by portable FTIR instruments, offering a decisive advancement for in situ analytical characterization of the pigments used in wall-paintings.