The work presented in this paper is part of a wider research project, which aims at documenting and analyzing stained glass windows by means of hyperspectral imaging. This technique shares some similarities with UV-VIS-IR spectroscopy, as they both provide spectral information; however, spectral imaging has the additional advantage of providing spatial information, since a spectrum can be collected in each pixel of the image. Compared to UV-VIS-IR spectroscopy, spectral imaging has rarely been used for the investigation of stained glass windows. One of the objectives of this paper is, thus, to compare the performance of these two instruments to validate the results of hyperspectral imaging. The second objective is to evaluate the potential of analyzing colored-glass pieces in reflectance modality and compare the results with those obtained in transmittance, in order to highlight the differences and similarities between the two approaches. The geometry of the systems and the backing material for the glass, as well as the characteristics of the glass pieces, are discussed. L*a*b* values obtained from the spectra, as well as the calculated color difference ΔE00, are provided, to show the degree of agreement between the instruments and the two measurement modalities.