This paper reports the preliminary diagnostic survey of the six controversial mural paintings painted in 1946–49 at the Maritime Station of Rocha do Conde de Óbidos in Lisbon, considered the artistic epitome of Almada Negreiros mural painting art. Four research questions drove this research: a) What are the main decay phenomena present and their sources? b) Which are the paint layers most affected, and are they linked to a particular pigment? c) Is there any relation between the painting technique used and the deterioration or stability of the paint layers and pigments? And finally, d) Are there differences in the decay phenomena present in both maritime stations of Alcântara? The analytical setup comprised in-situ and laboratory analysis by way of technical photography documentation (TP), handled optical microscopy (h-OM), handheld X-Ray Fluorescence (XRF), complemented by optical microscopy of microfragments and cross sections (OM-Vis-UV), X-Ray Diffraction (XRD), and Scanning Electron Microscopy coupled with Energy Dispersive Spectroscopy (SEM-EDS).The first results indicate flaking of the paint layers as the main and most severe deterioration feature present in most of the murals. The yellow ochres, browns, blacks, and light greens are the colours most affected, showing different degrees of loss. The pictorial technique used, the presence and action of soluble salts in the structure, and even the products used as adhesives during past interventions might be the root of this phenomenon.