Various selenium (IV) complexes with essential amino acids such as phenylalanine, histidine, and tryptophan were encapsulated within polymeric matrices in hydrogel state based on collagen-starch, generating the biomatrices Col-St(Se-F), Col-St(Se-H), and Col-St(Se-T), respectively. 1 mg of each type of selenium complex was employed per mass ratio in matrices consisting of 60% collagen and 18% starch by mass. The advanced materials were surface-characterized using scanning electron microscopy (SEM), and their properties such as swelling capacity and degradation rate in commercial vegetable substrate were also evaluated. The amino acid involved in the selenium complex forms characteristic granules that determine the microstructure and porosity of the biomatrix; reporting that in the case of all biomatrices with selenium complexes, swelling capacities exceeding 2900% are shown, resulting statistically significant compared to the sole collagen-starch matrix. Likewise, the matrices exhibit resistance to degradation in the presence of the commercial vegetable substrate for up to 30 days of evaluation. In vitro biocompatibility studies with green and red tomato cells derived from fresh seeds reveal that the biomatrices Col-Str(Se-F) and Col-Str(Se-H) overstimulate the metabolism of green tomato cells, while for red tomato cells, greater stimulation is appreciated in the Col-Str(Se-T) biomatrix. The chemical composition of the biomatrices promotes the proliferation of these types of plant cells as inspected by epifluorescent microscopy. Such advanced materials could be successfully applied in agricultural applications related to tomato cultivation by regulating water capacity, substrate biodegradation, and stimulated metabolism to promote tomato growth.