For farmers the use of agrochemicals is the preferred method to control pests and diseases. Considering the market demand for biological control products, the encapsulation could be a competent alternative to current commercial formulations for cellular viability and controlled release. The purpose of this study was to use ionic gelation with sodium alginate, starch and maltodextrin to immobilize Bacillus subtilis and to evaluate the biocontrol effect against Fusarium oxysporum f. sp. lycopersici in vitro. The matrix with a concentration of 2% sodium alginate, 1% starch, and 1% maltodextrin is a suitable method for cellular viability and biological control activity against Fusarium oxysporum f. sp. lycopersici, with a reduction of mycelial growth of 49.6% and a survival rate for Bacillus subtilis of 98.05% (p less than 0.0001).The use of immobilized bacteria as biological control agents are sustainable and effective bio-inputs that could be used at industrial scale and benefit the tomato crops against attack by Fusarium oxysporum f. sp. lycopersici.