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The Joint United Nations Programme on HIV/AIDS has set ambitious targets to improve diagnosis and treatment rates, aiming for 95% of people living with HIV to know their status and 95% of those diagnosed to be on sustained antiretroviral treatment, and 95% of those on treatment to achieve viral suppression. However, challenges persist, especially concerning the HIV Viral Load (VL)/Early Infant Diagnosis (EID) testing coverage and commodity availability, leading to stock-outs and delays in testing processes. This study assessed the factors influencing commodity availability and testing platform performance in public health facilities. A mixed methods study design was employed, integrating both quantitative and qualitative data collection methods concurrently. Primary and secondary data were collected using a structured data abstraction form applied to stock cards, stock books, and Point-of-Care (POC) data systems to obtain HIV VL and EID POC consumption data for the financial year 2023/2024 (July 2023–June 2024). The study covered all 22 public health facilities in the Masaka region providing HIV VL and EID POC testing services. In-depth interviews, guided by an interview guide, were conducted with healthcare workers to capture factors affecting HIV EID/VL POC testing commodities and platform performance. STATA 15.0 was used for quantitative data analysis, while thematic analysis was used for qualitative data. The average stock-out duration per month was 9 days for VL POC cartridges and 8 days for EID POC cartridges. Most of the facilities 13/22 (59%) experienced EID cartridge stock-outs for fewer than 5 days per month, while 6/22 (27%) faced stock-outs exceeding 10 days. Similarly, 13/22 59% of facilities had VL POC cartridge shortages for fewer than 5 days, whereas 7/22 (32%) experienced stock-outs for more than 10 days. Stock availability was significantly associated with increased detection of HIV positivity. Qualitative interviews indicated that stock-outs were often driven by supply chain delays, funding constraints, and challenges in forecasting and procurement. One laboratory manager noted: “Sometimes we wait weeks for cartridges to be supplied, which affects our ability to test on schedule.” The mean equipment utilization rate was 47%, with only 4/22 (18%) of facilities achieving optimal utilization. Factors significantly influencing POC platform performance included device type (aOR = 3.3; 95% CI: 1.06–9.96; p = 0.039), positivity rate (aOR = 12; 95% CI: 1.56–92.3; p-value = 0.017), sample error rate (aOR = 5; 95% CI: 1.45–17.27; p = 0.01), and frequent result uploads to national systems (aOR = 3.8; 95% CI: 1.24–11.29; p = 0.019). Qualitative findings reinforced these results: staff cited equipment downtime, cartridge shortages, and limited training as barriers to optimal utilization. A respondent explained: “We sometimes have machines but not enough trained staff to run them efficiently, or they break down and repairs take time.” The findings highlight persistent supply chain inefficiencies, with some facilities experiencing prolonged stock-outs. Low platform utilization was driven by equipment downtime, cartridge shortages, and inadequate staff training. Key challenges included supply chain delays, funding constraints, infrastructure gaps, and staffing shortages. Strengthening forecasting, procurement, distribution, and staff training alongside better coordination and infrastructure investment will be crucial for improving POC testing services and enhancing early HIV diagnosis.