Italian cuisine and its traditional recipes experience an ever-increasing popularity around the world. The “Integrated Approach” is the key to modern food research and the innovative challenge for analyzing and modeling agro-food systems in their totality. The present study aims at applying and evaluating Fourier Transformed Infrared (FTIR) spectroscopy for the analysis of complex food matrices and food preparations. Nine traditional Italian recipes, including First courses, One-dish meals, Side courses, and Desserts, were selected and experimentally prepared. Prior to their analysis via FTIR spectroscopy, the samples were homogenized and lyophilized. The IR spectroscopic characterization and the assignment of the main bands was carried out. Numerous peaks, which correspond to functional groups and modes of vibration of the individual components, were highlighted. The spectra are affected by both the preparation procedures, the cooking methods, and the cooking time. The qualitative analysis of the major functional groups can serve as a basis for a discrimination of the products and the investigation of fraud. For this purpose, the FTIR spectra were evaluated using Principal Component Analysis (PCA). Our results show how the utilization of vibrational spectroscopy combined with a well-established chemometric data analysis method represents a potentially powerful tool in research linked to the food sector and beyond. This study is a first step towards the development of new indicators of food quality.