Research concerning the formation and removal of black crusts on various historical objects is approached from many different angles. The so-called “yellowing effect”, observed after laser treatment for cleaning purposes, has also received a lot of attention. Evidence regarding this phenomenon differs considerably and the actual mechanisms are still speculated on by researchers. In an attempt to elucidate the processes involved in the yellowing effect associated with laser cleaning, a new analytical technique has been used to investigate the black crust, a region of the sample cleaned by laser irradiation at 1064 nm and another region of the same sample subjected to further laser irradiation at 355 nm, on a limestone sample from the cathedral of Seville in Spain. Micro-Raman spectrometry offers the advantage of spatial chemical characterization of the stone, based upon its molecular makeup and was performed on the bulk body of the stone. Raman and scanning electron microscopy/energy dispersive X-ray spectrometry (SEM/EDXS) results indicate that the surfaces cleaned by irradiation at 1064 nm and by double irradiation at 1064 and 355 nm differed in terms of their calcium sulphate, calcium oxalate and iron oxide content, and that this could contribute to the difference in colour observed.