Sixteen semi-hard cheeses varying by their protein (20.2–24.1%), fat (23.7–31.1%) and dry matter (50.2–57.9%) contents were manufactured and ripened in controlled conditions. Fluorescence (vitamin A) and mid-infrared (2780–3000 cm−1 region) spectra were collected on the 16 different cheeses at 1, 21, 51 and 81 days of ripening. The data tables containing the mid-infrared and fluorescence spectra of the different cheeses were analyzed by principal component analysis and canonical correlation analysis methods. The obtained similarity maps showed that it was possible to discriminate the cheeses at the four different ripening times from the infrared and fluorescence spectra. In addition, the interest to combine the two spectroscopies was demonstrated since a better discrimination of the four stages was obtained using canonical correlation analysis. The examination of the spectral patterns associated with the principal components and the canonical variates showed that the structure of triglycerides acyl chains in fat globules was modified during cheeses ripening. The shift of the methylene bands in the infrared region and the changes of the shape of vitamin A fluorescence spectra agree with partial crystallization of triglycerides from 21 to 81 days of storage.