Background: Several changes must be made to the services to ensure patient safety and enable delivering services in environments where the danger of infection of healthcare personnel and patients in primary care (PC) institutions is elevated, i.e., during the COVID-19 pandemic. Objective: This study aimed to examine patient safety and healthcare service management in PHC practices in Kosovo during the COVID-19 pandemic. Methods: In this cross-sectional study, data were collected using a self-reported questionnaire among 77 PHC practices. Results: Our main finding reveals a safer organization of PC practices and services since the COVID-19 pandemic compared to the previous period before the pandemic. The study also shows a collaboration between PC practices in the close neighborhood and more proper human resource management due to COVID-19 suspicion or infection. Over 80% of the participating PC practices felt the need to introduce changes to the structure of their practice. Regarding infection protection measures (IPC), our study found that health professionals’ practices of wearing a ring or bracelet and wearing nail polish improved during the COVID-19 pandemic compared to the pre-pandemic period. During the COVID-19 pandemic, PC practice health professionals had less time to routinely review guidelines or medical literature. Despite this, implementing triage protocols over the phone has yet to be applied at the intended level by PC practices in Kosovo. Conclusions: Primary care practices in Kosovo responded to the COVID-19 pandemic crisis by modifying how they organize their work, implementing procedures for infection control, and enhancing patient safety.