The application of biopesticides in many industries can be hampered due to their high volatility, susceptibility to degradation when exposed to light or microbial activity, and reduced activity when exposed to stressful environmental conditions. Microencapsulation of biopesticides is a promising technique to solve and address such problems. This study aimed to encapsulate and characterize the extracts produced by Penicillium chrysogenum R1 and evaluate their antifungal activity in the plant assay. The capsules were prepared with a chitosan (0.5 mg/mL) and sodium alginate solution (2% w/v), and 20% (v/v) cell‐free extract recovered from the P. chrysogenum R1 fermentation. The capsules were synthesized in a 2.5% CaCl2 solution at room temperature. The capsules were characterized by DLS and SEM. To determine the efficiency of the free and encapsulated extract, they were applied to tomato plants infected with Fusarium oxysporum. Once the symptoms were observed, the severity and incidence of the disease, as well as the morphological parameters were evaluated. such as dry weight of aerial and root biomass, plant height, root length, stem diameter, chlorophyll content, and number of leaflets. The extract produced by P. chrysogenum R1 was encapsulated in chitosan/alginate capsules with a size range of around 300 nm. The free and encapsulated extracts allowed to efficiently control the disease caused by F. oxysporum and the development of the plants. Therefore, the extract produced by P. chrysogenum R1 encapsulated in chitosan/alginate can effectively control tomato vascular wilt caused by F. oxysporum under greenhouse conditions, promoting plant growth.