OBJECTIVE: Our New York City Municipal Public Health System-based multisite ambulatory and school-based Gotham Health clinics offer waived point-of-care tests and provider-performed microscopy to the local communities. Our Gotham Health laboratory service conducts system-wide centralized implementation, monitoring, and oversight of the POCT operations. Laboratory staffing has always been an issue for us as there is a decades-long shortage of laboratory staff, primarily licensed medical technologists and technicians, in New York, like many other states. Our clinical laboratory operations team struggled to hire qualified people even before the COVID-19 pandemic onset. It has faced more significant challenges with the emergence of SARS-CoV-2 pandemic cases in New York City and across the country since mid-March 2020. METHODS: As staffing continues to be a struggle, it directly affected the POCT performances and a system-wide reduction in the test numbers during the pandemic. We investigated to identify the factors that made staffing more challenging. RESULTS: The impact on our POCT started after laboratory staff relocated to the acute care hospital laboratories to provide testing support during the pandemic's peak. That caused significant delays or complete cessation of POCT operations in the clinics due to a lack of oversight support. We also experienced the risk of more vacated positions where staff already feel overworked, overwhelmed, and emotionally drained, causing professional burnout. The significant challenges identified are noncompliance with vaccine mandates resulting in job dismissal and voluntary resignations in exchange for higher-paying laboratories. Finally, the other challenges identified were frequent sick calls due to mental fatigue, retirement of seasoned staff, and inability to attract qualified technologists to meet the demands of increasing test-ordering patterns. CONCLUSIONS: Determining the factors that culminated in the staffing issues becoming more challenging during the COVID-19 pandemic in our ambulatory care clinic laboratory operations will help us in future crisis planning and mitigation.