The monitoring of stone alteration represents a key factor in the knowledge and prediction of the status of conservation of building stones in the urban framework. A continuous monitoring requires a non-destructive analytical approach and, possibly, a simple, low-cost and effective tool to study the decay processes. Previous studies demonstrated the capability of the SWIR hyperspectral technique to gain information on the degree of sulfation of carbonate stone surfaces. In this study we aim at setting up a protocol to investigate on-site the sulfation degree of the white marble cladding surfaces of the worldwide-famous Santa Maria del Fiore Cathedral in Florence (Italy). The proposed protocol couples information by SWIR hyperspectral and colorimetric techniques. We have proved that, in selected areas investigated at a distance of nine years, the colour and the mineralogical changes (i.e., sulfation) are significantly greater than the relative uncertainties of the two methods. Moreover, the proposed protocol results rapid, repeatable and fully not invasive.