The use of agro-industrial waste from Haden mango (Mangifera indica L.) and red bean (Phaseolus vulgaris) residues was explored for bioencapsulation with bioremediation purposes. Pectin and protein were extracted from mango and red bean, respectively, and used in addition to sodium alginate as materials for the formulation, through an augmented mixture design experiment with a variable process (pH), of a soluble ternary biopolymer system for encapsulation of microorganisms. The capsules were physically and thermally characterized and evaluated with a bacteria consortium for hydrocarbon bioremediation. The bioremediation assays, one with hexadecane and the other with diesel resulted in a hydrocarbon uptake increase (5% for hexadecane, 10% for diesel) and shorter consumption times (4 days less for hexadecane and 3 days less for diesel) compared to their respective control without encapsulation. The novelty of this work lies in the interdisciplinary approach to the utilization of materials from cheap sources for bioencapsulation with applications in different areas. Insights into the mass transfer of the capsules were also obtained as the first step into further studies. •Agro-industrial residues for encapsulation of microorganisms in bioremediation.•Optimization of the encapsulation formulation through a mixture design experiment.•Biocapsules composed mainly of bean protein as a nitrogen source.