The quantitative determination of moganite in flint and chert plays an important role in the characterisation of these silica rocks and in the study of their genesis and evolution. Both Raman and infrared (IR) spectroscopy promise to be rapid and cost-effective tools for such studies. However, the use of vibrational spectra of moganite in silica rocks is hampered by the proximity of specific moganite bands with IR and Raman vibrations bands of non-bridging Si-O in silanol (SiOH) groups of chalcedony, the main coexisting silica phase. This may result in spectral interferences that lead to an overestimation of the moganite concentration. In order to calibrate quantitative moganite detection using IR and Raman spectroscopy, the spectra of chalcedony/moganite mixtures were studied using spectral decomposition. Heat treatment of the samples prior to their analysis is found to reduce the contribution of chalcedony silanol-bands to the measurement of the moganite bands, facilitating in this way the interpretation of the spectra. A new calibration curve is proposed for quantitative moganite detection using Raman spectroscopy. Infrared spectroscopy is also found to be useful for moganite quantification: a molar absorption coefficient of 43 L/mol·cm for the specific moganite-band at 575 cm−1 is derived for the first time. The exact position of the specific IR and Raman moganite-bands is found to depend on whether the mineral occurs intermixed with chalcedony or in pure form. This study opens new prospects for quantitative moganite detection in silica rocks using vibrational spectroscopy.