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Background Initiating and retaining HIV-exposed infants on antiretroviral therapy (ART) before 12 weeks of age remains a pressing public health concern in Malawi and other Sub-Saharan African countries. Despite its known benefits in reducing mortality and morbidity, challenges persist, including long turnaround times (TAT) for Deoxyribonucleic Acid Polymerase Chain Reaction (DNA-PCR) results, negative caregiver perspectives and healthcare-worker barriers. This report discusses the potential of integrating different data collection methods in laboratory information systems to reduce TAT between testing and ART initiation.Methods To address delays in the Malawi National Laboratory Information Management System (NLIMS), we integrated NLIMS into the electronic medical records (EMRs). We conducted this activity between November 2022 and June 2023 at the Elizabeth Glaser Paediatric AIDS Foundation in Malawi.Results The integrated NLIMS featured offline capabilities, barcode standardisation and efficient order pulling from previously independent workflows. Electronic transmission to EMRs improved the efficiency of transmitting test statuses online. The average TAT decreased by 65 days (from 77 to 12 days) during months with both lower and higher testing volumes ranging from 2595 to 5349 samples.Conclusions Integrating data collection workflows significantly reduced TAT, demonstrating a non-random variation and overall improvement. Future studies should explore algorithms, workflows and modules that alert healthcare providers and caregivers of the critical therapeutic point before 12 weeks.