Several mortars from mural paintings were collected from the Misericórdia Church of Odemira and analysed by using different techniques namely X-ray diffraction, thermogravimetric analysis with differential thermal analysis, SEM-EDX, optical microscopy, CHNS elemental analysis and chemical analysis. Microfragments of paint layers were collected and analysed by microchemical analysis. The results showed that the mortars are aerial lime mortars with siliceous aggregates and that the pigments used were mainly pigments from local sources (red and yellow ochre’s and malachite) and small blue.