OBJECTIVE: This study aimed to investigate the challenges in implementing a Zambian electronic health records (EHR) system labelled 'SmartCare' from diverse stakeholder perspectives in order to improve prevention of mother-to-child transmission (PMTCT) data collection so that SmartCare can be used for clinic performance strengthening and programme monitoring. DESIGN: This is a qualitative retrospective study. SETTING AND PARTICIPANTS: SmartCare is a Zambian Ministry of Health (MoH)-led project funded by the US Centre for Disease Control and Prevention. Data were collected using in-depth interviews, observations and focus group discussions (FGDs) between September and November 2016. Seventeen in-depth interviews were held with a range of key informants from the MoH and local and international organisations implementing SmartCare. Four data entry observations and three FGDs with 22 pregnant and lactating women seeking PMTCT services were conducted. Data were analysed using a thematic content approach. RESULTS: The SmartCare system has evolved from various patient tracking systems into a multifunctional system. There is a burden of information required so that sometimes not all is collected and entered into the database, resulting in poor data quality. Funding challenges impede data collection due to manpower constraints and shortages of supplies. Challenges associated with data collection depend on whether a paper-based or computer-based system is used. There is no uniformity in the data quality verification and submission strategies employed by various IPs. There is little feedback from the EHR system at health facility level, which has led to disengagement as stakeholders do not see the importance of the system. CONCLUSION: SmartCare has structural challenges which can be traced from its development. Funding gaps have resulted in staffing and data collection disparities within IPs. The lack of feedback from the system has also led to complacency at the operational level, which has resulted in poor data quality in later years.