Non-communicable Diseases (NCDs) are the leading cause of global mortality and disability with a rising burden in low- and middle-income countries. Their multifactorial aetiology, and their requirement of long-term care, implies the need for comprehensive approaches. From 2009, the Ministry of Health (MoH) in El Salvador has developed a national public health system based on comprehensive primary health care. This study aims to describe the different stakeholders' perceptions about the management of NCDs along the pathways of care in this health system. During three fieldwork periods in 2018, three complementary qualitative data collection methods were deployed and conducted in settings with high prevalence of NCDs within El Salvador. First, illness narrative methodology was used to document the life histories of people living with a chronic disease and being treated in second and third level health facilities. Second, through social mapping, support resources that NCD patients used throughout the process of their illness within the same settings were analysed. Third, semi-structured interviews were conducted in the same locations, with both chronic patients and health personnel working at different levels of the primary health care setting. Participants were recruited through purposive and snowball sampling, and a deductive approach was implemented for coding during the analysis phase. After grouping codes into potential themes, a thematic framework was developed using a reflexive approach and following triangulation of the data. This innovative approach of combining three well-defined qualitative methods identified key implications for the implementation of a comprehensive approach to NCD management in resource-poor settings. The following elements are identified: 1) social risk factors and barriers to care; 2) patient pathways to NCD care; 3) available resources identified through social connections mapping; 4) trust in social connections; and 5) community health promotion and NCD prevention management. The Salvadoran public health system has been able to strengthen its comprehensive approach to NCDs, combining a clinical approach - including long-term follow-up - with a preventive community-based strategy. The structural collaboration between the health system and the (self-) organised community has been essential for identifying failings, discuss tensions and work out adapted solutions.