Background Non-communicable diseases (NCDs), particularly hypertension and diabetes, represent a rising public health burden in India, driven by lifestyle changes and complex social determinants. In Chamarajanagar district in southern Karnataka, our previous findings and related studies 21’ suggest the prevalence of NCDs is rising alongside systemic gaps in the continuum of care and multisectoral action. The IMPACT NCD implementation research study aims to strengthen primary healthcare capacity for the continuum of care and foster multisectoral collaboration for effective NCD prevention and management. By investigating the causal pathways and contextual dynamics of these interventions, the study uncovers how and under what circumstances such strategies succeed. Methodology The study is guided by a theory-driven implementation research design. Interventions developed using a participatory approach, includes two main components: Capacity building combined with technical and hands-on support for healthcare workers at Ayushman Arogya Mandirs (AAMs) on NCD screening, follow-up, and the continuum of care. Sensitisation workshops for local elected officials, police personnel, and students in grades 8 to 12. Implementation dimensions including practical adoption and fidelity are assessed using a sequential explanatory mixed-methods approach. Routine quantitative programme data will be analysed using Latent Profile Analysis to stratify primary units by performance. A purposive sample of high-performing and low-performing units will be selected for in-depth qualitative analysis through interviews and observations to test and refine the initial Theory of Change. Discussion Moving beyond measuring clinical outcomes to exploring the underlying processes and contextual factors, the study identifies generative mechanisms that drive implementation success. This approach provides contextual evidence on how complex multisectoral NCD programmes can be embedded within existing government systems.