Abstract Background General practitioners often act as gatekeeper, authorizing patients’ access to hospital care. This gatekeeping role became even more important during the current COVID-19 crisis as uncertainties regarding COVID-19 made estimating the desirability of hospital referrals (for outpatient or inpatient hospitalization) complex, both for COVID and non-COVID suspected patients. This study explored Dutch general practitioners’ experiences and ethical dilemmas faced in decision making about hospital referrals in times of the COVID-19 pandemic. Methods Semi-structured interviews with Dutch general practitioners working in the Netherlands were conducted. Participants were recruited via purposive sampling. Thematic analysis was conducted using content coding. Results Fifteen interviews were conducted, identifying four themes: one overarching regarding (1) COVID-19 uncertainties, and three themes about experienced ethical dilemmas: (2) the patients’ self-determination vs. the general practitioners’ paternalism, (3) the general practitioners’ duty of care vs. the general practitioners’ autonomy rights, (4) the general practitioners’ duty of care vs. adequate care provision. Conclusions Lack of knowledge about COVID-19, risks to infect loved ones, scarcity of hospital beds and loneliness of patients during hospital admission were central in dilemmas experienced. When developing guidelines for future crises, this should be taken into account.