Background In Slovenia, primary care is the backbone and gatekeeper to the health care system. During the first months of the COVID-19 pandemic, primary care had to be reorganised to manage suspected COVID-19 patients, safely care for other patients, and manage the consequences of the pandemic. Objectives To explore the opinions and experiences of Slovenian primary care workers (PCWs) about their confrontation with COVID-19. Methods In June 2020, we conducted a qualitative study among PCWs in Slovenia. Invited participants ( n = 42) worked either in primary health care centres or as private contractors and were involved in organising care during the COVID-19 pandemic. The study was conducted using semi-structured online questionnaires. Data was analysed using an inductive-deductive method. Results Out of 42 invited subjects, 18 participated in the study. The main predefined categories were Information/from decision-makers, Organisation of work, Workforce, Personal protective equipment, Views on decision-making institutions, Stressors that place additional burden on health workers, and Suggestions for improvement (funding, organisation of care). Within these categories, 29 themes emerged. Conclusion Based on participants’ experiences and suggestions, the most important areas to address in similar pandemic situations are clear organisation of work in primary care (adequate funding, staff allocation, distribution of personal protective equipment), psychological solid support for health workers, and effective and timely support from health authorities.