Food packaging plays an active role in the environment/packaging/food system, and new solutions take into account new concepts of smart, active, and/or eco-friendly food packaging materials. On this point of view, the active packaging system should be capable of interacting with the food, for instance by the release of active molecules that will provide protection against microbial spoilage, and simultaneously be ‘natural’. A full exploitation of the antimicrobial and antioxidant properties of propolis, in order to achieve a significant prolongation of the shelf-life, can meet these needs. Moreover, fast methods able for classifying, sorting, and identifying the quality and the stability characteristics associated with the different materials are requested along the food chain in order to validate their properties. This study aimed the identification of bioactive compounds from Italian propolis in smart packaging materials by applying the aquaphotomics approach. The Aquagrams results highlighted that the absorption differences at 1410 nm are able to identify the paper sheets obtained by the incorporation of the active compounds. A second Aquagrams plot was built up for sheets measured on polythene layer. Results showed different water patterns at 1438, 1440, and from 1474 to 1518 nm. These data confirm that the water absorption in NIR range can be affected by the presence of chemical groups derived from the active compounds of propolis, which are able to interact with water spectral response.