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Background Four decades after the Alma-Ata Declaration, strengthening primary health care (PHC) remains a priority for health systems, especially in low- and middle-income countries (LMICs). Given the prominence of chronic diseases as a global health issue, PHC must include a wide range of components in order to provide adequate care. Objective To assess PHC preparedness to provide chronic care in Mozambique, Nepal and Peru, we used, as ‘tracer conditions’, diabetes, hypertension and a country-specific neglected tropical disease with chronic sequelae in each country. Methods By implementing a health system assessment, we collected quantitative and qualitative data from primary and secondary sources, including interviews of key informants at three health-system levels (macro, meso and micro). The World Health Organization’s health-system building blocks provided the basis for content analysis. Results In total, we conducted 227 interviews. Our findings show that the ambitious policies targeting specific diseases lack the support of technical, administrative and financial resources. Data collection systems do not allow the monitoring of individual patients or provide the health system with the information it requires. Patients receive limited disease-specific information. Clinical guidelines and training are either non-existent or not adapted to local contexts. Availability of medicines and diagnostic tests at the PHC level is an issue. Although medicines available through the public health care system are affordable, some essential medicines suffer shortages or are not available to PHC providers. This need, along with a lack of clear referral procedures and available transportation, generates financial issues for individuals and affects access to health care. Conclusion PHC in these LMICs is not well prepared to provide adequate care for chronic diseases. Improving PHC to attain universal health coverage requires strengthening the identified weaknesses across health-system building blocks.