question: Background: Reports describing post-vaccine autoimmune phenomena, in previously healthy individuals, increased the concerns regarding the risk of disease flare-ups in patients with immune diseases. We aimed to assess the potential risk of disease flare-up, after receiving the COVID-19 (Coronavirus disease 2019) vaccine, during a follow-up period of 6 months. Methods: We performed a prospective cohort study, enrolling the patients with autoimmune- and immune-mediated diseases who voluntarily completed our questionnaire, both online and during hospital evaluations. Based on their decision to receive the vaccine, the patients were divided into two groups (vaccinated and non-vaccinated). Participants who chose not to receive the vaccine served as a control group in terms of flare-ups. Results: A total of 623 patients, 416 vaccinated and 207 non-vaccinated, were included in the study during hospital evaluations (222/623) and after online (401/623) enrolment. There was no difference concerning the risk of flare-up between vaccinated and non-vaccinated patients (1.16, versus 1.72 flare-ups/100 patients-months, p = 0.245). The flare-ups were associated with having more than one immune disease, and with a previous flare-up during the past year. Conclusions: We did not find an increased risk of flare-up following COVID-19 vaccination in patients with autoimmune-/immune-mediated diseases, after a median follow-up of 5.9 months. According to our results, there should not be an obvious reason for vaccine hesitancy among this category of patients.