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Context Acidic soil stress is a silent threat to the plant biome including rice. Aim To develop a feasible method for ameliorating acidic soil stress that neutralises the acidity and benefits the plants to restore the necessary nutrients in the soil environment in an eco-friendly approach. Methods A traditionally prepared organic biochar from stem, peel and suckers of banana, i.e. kolakhar was used individually and also in a combination with commercial biochar (biokhar) to evaluate the growth of five traditional rice varieties with contrasting characters for tolerability of Al toxicity and P deficiency. Key Results The rice seedlings treated with kolakhar showed better responses in biomass, photosynthetic efficiency and antioxidant protection mechanisms. Enhanced production of ascorbate peroxidase, guaiacol peroxidase etc. in seedlings growing under kolakhar treated soil reveals their possible mechanism developed to cope with the stress. The final pH of all the treated soils with ameliorants was found to change to ∼6.0, nearly similar to normal soil from 4.2 to 4.5. The amount of phosphorous was highest in soil treated with kolakhar 250 mg kg−1. Kolakhar showed the highest reduction of available Al from 2.107 to 0.018 mg kg−1 after 30 days of treatment. Above all, the histochemical staining elucidated that the Al uptake was more profound in the controls. In contrast, much reduced Al uptake was observed in roots under treatment with ameliorants, which could be because of the decreased Al content in the soil as determined by inductively coupled plasma optical emission spectroscopy (ICP-OES) analysis. Conclusions These findings have paved the way to overcome the severe issues of acidic soil stress, associated hazards of Al accumulation and other stresses. Implications Kolakhar could be exploited for ameliorating soil acidity through low cost and eco-friendly way.