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Garambullo is a plant with little industrial application. However, garambullo contains betalains, photosensitive phytochemical compounds, which through microencapsulation can be used in chitosan–polyvinyl alcohol (PVOH) films for application in tomato coatings. These biopackages were characterized by physical tests, water vapor permeability, puncture tests, extension, color, differential scanning calorimetry (DCS), Fourier transform infrared (FTIR) spectroscopy, and antioxidant and antimicrobial activity analyses. The influence of the biopackages on the tomato coatings was measured using parameters such as minimum weight loss close to 2% at day 9, pH of 4.6, Brix of 5.5, titratable acidity of 1 g acid/100 mL sample, and shelf life of up to 18 days. The biopackages containing betalain microcapsules had a water vapor permeability of 2 × 10−14 g/h·m·Pa and an elongation of 5 ± 0.5%, indicating that the package did not stretch. The deformation at the breaking point for the package without and with microcapsules was 0.569 and 1.620, respectively. With respect to color, adding white microcapsules and betalains can cause the material to darken, resulting in a yellowish color. Furthermore, the phenolic content was greater for the biopackages with betalains, while there was no significant difference in the antioxidant activity since the active compounds were not released. According to the in vitro results, the inhibition of B. cinerea was achieved on the eighth day when the active compounds were released from the microcapsules. The tomato with betalains lost 2% of its weight, and B. cinerea was inhibited, extending its shelf life to 18 days. The proposed biopackages have good properties as biopolymers and inhibit the presence of B. cinerea.