This work reports the use of a portable Raman microprobe spectrometer for the analysis of bulk and decaying compounds in carbonaceous materials such as stones, mortars and wall paintings. The analysed stones include limestone, dolomite and carbonaceous sandstone, gypsum and calcium oxalate, both mono- and dihydrated, being the main inorganic degradation products detected. Mortars include bulk phases with pure gypsum, calcite and mixtures of both or with sand, soluble salts being the most important degradation products. The pigments detected in several wall paintings include Prussian blue, iron oxide red, iron oxide yellow, vermilion, carbon black and lead white. Three different decaying processes have been characterised in the mortars of the wall paintings: (a) a massive absorption of nitrates that reacted with calcium carbonate and promoted the unbinding of pigment grains, (b) the formation of black crusts in the vault of the presbytery and (c) the thermodecomposition of pigments due to a fire.