The development of eco-friendly biocontrol solutions is critical to reducing reliance on synthetic fungicides, which contribute to environmental pollution, pathogen resistance and health hazards. This study investigates the encapsulation of Trichoderma harzianum, a beneficial fungal biocontrol agent, within alginate-bentonite (BNT) clay composite beads to enhance its stability and efficacy. Sodium alginate served as the primary matrix, while BNT clay was incorporated to improve mechanical strength and thermal resistance. The resulting microbeads exhibited uniform morphology, ensuring effective protection and sustained release of fungal conidia under varying environmental conditions. Structural and thermal properties were analysed using Fourier-transform infrared spectroscopy (FTIR), Scanning electron microscopy (SEM) and Thermogravimetric analysis (TGA), confirming the composite’s durability and heat tolerance. Encapsulated conidia maintained high viability over six months, demonstrating the formulation’s potential for long-term storage. The findings suggest that alginate-BNT encapsulation significantly improves the shelf life and field performance of microbial pesticides, offering a viable alternative to chemical treatments. By combining biopolymer science with clay-based enhancements, this research contributes to sustainable crop protection strategies. The proposed method aligns with green chemistry principles, providing a scalable solution for agricultural applications while minimising ecological impact.