Abstract Biological control (BCAs) such as Trichoderma spp. minimize fungicides inputs in agriculture, and increase both the plant nutrition and the efficacy against fungal diseases. Novel bioproducts in crop management are called to guarantee sustainable antagonism activity of BCAs and increase the acceptance of the farmers. The encapsulation in polymeric matrices play a prominent role for providing an effective carrier/protector and long-lasting bioproduct. This research aimed to compare two hydrogel capsules prototypes based on alginate (P1) and amidated pectin (P2), containing Trichoderma koningiopsis Th003 conidia. Capsules were prepared by the ionic gelation method and calcium gluconate as crosslinker was used. The capsules were characterized by various properties such as conidia releasing at different pH values, drying conidia survival, storage stability, and biocontrol activity against sheath blight (R. solani) in rice. P2 prototype provided higher survival to Th003 up to 98% in fluid bed drying, faster conidia release at pH 5.8, storage stability > 6 months at 18°C, and a disease reduction up to 67%. Amidated pectin provides advantages on drying survival and conidia release at pH 5.8. Both biopolymers facilitate the antagonistic activity against R. solani, and therefore can be incorporated in hydrogel capsules for novel bioinoculants development. This research highlights the knowledge regarding the influence of biopolymer in hydrogel capsules on survival and shelf-life of Trichoderma spp conidia.