Flashed glasses are composed of a base glass and a thin colored layer and have been used since medieval times in stained glass windows. Their study can be challenging because of their complex composition and multilayer structure. In the present work, a set of optical and spectroscopic techniques have been used for the characterization of a representative set of flashed glasses commonly used in the manufacture of stained glass windows. The structural and chemical composition of the pieces were investigated by optical microscopy, field emission scanning electron microscopy-energy dispersive X-ray spectrometry (FESEM-EDS), UV-Vis-IR spectroscopy, laser-induced breakdown spectroscopy (LIBS), and laser-induced fluorescence (LIF). Optical microscopy and FESEM-EDS allowed the determination of the thicknesses of the colored layers, while LIBS, EDS, UV-Vis-IR, and LIF spectroscopies served for elemental, molecular, and chromophores characterization of the base glasses and colored layers. Results obtained using the micro-invasive LIBS technique were compared with those retrieved by the cross-sectional technique FESEM-EDS, which requires sample taking, and showed significant consistency and agreement. In addition, LIBS results revealed the presence of additional elements in the composition of flashed glasses that could not be detected by FESEM-EDS. The combination of UV-Vis-IR and LIF results allowed precise chemical identification of chromophores responsible for the flashed glass coloration.