Low and Middle Income Countries are facing an epidemiological transition, with increases in the prevalence of and mortality related to Noncommunicable diseases. This burden of Noncommunicable diseases coexists in settings where important burdens of Communicable diseases still exist, leading to a double burden of disease. Health systems play a key role in the control and management for both Noncommunicable diseases and Neglected Tropical Diseases, which disproportionately affect poor and vulnerable populations, including women and children and their roles as carers. In Low and Middle Income Countries health systems are weak and these diseases have not received the funding and policy responses commensurate with their burden. Although political declarations exist addressing Noncommunicable diseases and Neglected Tropical Diseases and these highlight the importance of Primary Health Care and Universal Health Coverage in addressing these challenges, very little has been done to explore or develop action in this area. Research is therefore needed to develop context specific interventions to transform existing health systems to manage these conditions. The COmmunity HEalth System InnovatiON (COHESION) project being led by the Geneva University Hospitals and the University of Geneva in collaboration with partners in Mozambique, Nepal and Peru as well as other Swiss institutions will address this challenge through effective research, stakeholder engagement and appropriate interventions at the policy, health system and community level in order to sustainably improve the health of vulnerable populations. The research phases will combine multiple qualitative and quantitative research methods to assess: global and national policies; the health system at national level and in an urban/peri-urban and rural area with a focus on Primary Health Care; and in these same areas community barriers and enablers to Noncommunicable diseases and Neglected Tropical Diseases management. Results from this research will be communicated to different stakeholders using contextualised communication strategies adapted to each country. To develop the interventions for the COHESION project, we follow a co-creation process of designing the interventions with engagement from the target audience. The outcome of this will be a toolbox of interventions for policy, health system and communities targeted at Primary Health Care. One intervention from the overall toolbox will be tested in each country at the policy, health system and community levels. The intervention at the health system and community level may vary between the two settings in each country depending on the local circumstances and needs. Another aspect of the COHESION project will be the overall learning process in comparing these countries and settings throughout the research, intervention development and intervention implementation phases. These lessons and interventions will then be evaluated to propose both a conceptual model for addressing Noncommunicable diseases and Neglected Tropical Diseases as well as tailored plans for scale-up in each context.