This paper reports the diagnostic research of deteriorated paint layers from three mural panels made by Almada Negreiros found in the Alcântara Maritime Station in Lisbon. The aim was to understand the main decay phenomena to aid future conservation works. The methodology comprised in-situ analyses by technical photography in Vis, Vis-RaK and UVF, p-OM and h-EDXRF; micro sampling; OM, SEM-EDS, μ-XRD, μ-Raman, µ-FT-IR and Py-GC/MS. Preliminary results show that all the paint layers analyzed are affected by salts (alkali sulphates) that over time have caused flacking, lack of cohesion, erosion, and lacunae. The light greenish/greenish bluish paint layers in all three panels are the most affected. No organic binders were identified, only the presence of vinyl polymer in glossy paint surfaces.