It is expected that the population worldwide might exceed 9 billion by 2050, therefore it being imperative to increase food production. As such, the development of smart farming technology is an important key food production issue. In fact, through the use of UAVs (Unmanned Aerial Vehicles), it is possible to create normalized difference vegetation index (NDVI) maps, that can indicate factors, such as health and vegetation vigor. In this context, this study aimed to assess the state of three tomato varieties (beef heart, “chucha”, and apple) in the framework of a biofortification workflow with Fe and Zn, following an organic production mode. In a tomato experimental production field (GPS coordinates—39°41′48.517″ N; 8°35′45.524″ W), six foliar sprayings were carried out during the production cycle, with a mix of Zitrilon (15%) (0.40 and 1.20 kg·ha−1) and Maxiblend (1 and 4 kg·ha−1). NDVI was determined 7 days before the first foliar spraying and showed a maximum of 0.86 (on a scale from −1 to 1). After the 3rd foliar spraying, no changes were detected in the color of freshly harvest tomatoes (assessed through spectrophotometric colorimeter), but an increase of Fe and Zn content was found in the leaves, and of Zn in tomatoes themselves (except in “chucha” variety). The use of precision agriculture techniques in correlation with the other analyses is discussed.