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Background: Crop residue burning adversely affects air quality and consequently human health. India, being one of the largest agro-economies of the world, produces around 500 Million tonnes of crop residue annually most of which is burnt on-farm. However, integrated studies that simultaneously quantify the effects of crop residue burning while exploring the subjective determinants of the practice are lacking in India. This paper describes the protocol for a longitudinal mixed methods research study employing a community-based participatory approach to fill this gap.Methods: Both quantitative and qualitative data will be collected in a rural setting of the central Indian province of Madhya Pradesh, over 1 year. A steering committee comprising of the research team and community representatives will be formed. The proportion of cultivable land burnt in one crop burning season will be estimated. The association between crop residue burning, level of ambient air pollutants, and pulmonary function of village residents will be determined. Focus groups, interviews, and participatory rural appraisal methods will be used to explore stakeholder perspectives about crop residue burning. Potential barriers and opportunities for substituting burning with an alternative crop residue management technique will be ascertained as the basis for future interventions. Ethics approval has been obtained from the Institutional Ethics Committee of the National Institute for Research in Environmental Health (No: NIREH/BPL/IEC/2019-20/1494, dt 06/01/2020).Discussion: This manuscript describes the protocol for a novel community-based participatory study to investigate thoroughly the phenomenon of crop residue burning from the perspective of the agricultural community through their active collaboration. The lack of comprehensive evidence regarding the factors responsible for crop residue burning in India underlines the importance of implementing this study protocol to fill in this critical gap in knowledge. While acknowledging that findings of this study will be not generalizable to agricultural communities other than the one studied, it is expected that the study will generate baseline evidence that might be beneficial in developing and implementing an appropriate intervention strategy. [ABSTRACT FROM AUTHOR]