Background: With the increasing double burden of communicable and non-communicable diseases (NCDs) in sub-Saharan Africa, health systems require new approaches to organise and deliver services for patients requiring longterm care. There is increasing recognition of the need to integrate health services, with evidence supporting integration of HIV and NCD services through the reorganisation of health system inputs, across system levels. This study investigates current practices of delivering and implementing integrated care for chronically-ill patients in rural Malawi, focusing on the primary level. Methods: A qualitative study on chronic care in Phalombe district conducted between April 2016 and May 2017, with a sub-analysis performed on the data following a document analysis to understand the policy context and how integration is conceptualised in Malawi; structured observations in five of the 15 district health facilities, selected purposively to represent different levels of care (primary and secondary), and ownership (private and public). Fifteen interviews with healthcare providers and managers, purposively selected from the above facilities. Meetings with five non-governmental organisations to study their projects and support towards chronic care in Phalombe. Data were analysed using a thematic approach and managed in NVivo.Results: Our study found that, while policies supported integration of various disease-specific programmes at point of care, integration efforts on the ground were severely hampered by human and health resource challenges e.g. inadequate consultation rooms, erratic supplies especially for NCDs, and an overstretched health workforce. There were notable achievements, though most prominent at the secondary level e.g. the establishment of a combined NCD clinic, initiating NCD screening within HIV services, and initiatives for integrated information systems.