The church of San Pietro in Valle in Fano is with good reason considered one of the outstanding examples of baroque art in Central Italy. Currently the church is in a serious degradation status. For this reason, and in order to devise a correct conservative restoration project, a scientific study has been carried out, aimed at characterizing mortars used for the application of marble decorations and the different degradation products occurring in the church (i.e. pulverizations, encrustations, salt efflorescences, and condensation water). In the following, results obtained analyzing the different sample typologies by optical microscopy, X-ray diffraction, electron scanning microscopy with energy-dispersion micro-analytical system, ion chromatography, and head-space solid phase microextraction-gas chromatography-mass spectrometry will be reported.