Abstract Background To learn from the current crisis caused by the COVID-19 pandemic and be prepared for future pandemics, it is important to investigate the impact of this extraordinary period on the wellbeing of patients with inflammatory bowel disease (IBD). Therefore, the aim of this research was to describe the self-reported Health-Related Quality of Life (HRQoL) and disease control of patients with IBD from the start of the COVID-19 pandemic and measures in The Netherlands. Methods This was a prospective study initiated on March 17, 2020 until July 1st, 2020. All patients aged 18 years and older with IBD that visited the Erasmus MC (Rotterdam, The Netherlands) outpatient clinic between March 2019 to February 2020 received up to date information on COVID-19. Patients were invited to complete online questionnaires at week 0, 2, 6 and 12. The Inflammatory Bowel Disease Questionnaire (IBDQ), the Inflammatory Bowel Disease control-8 (IBD-control-8 and the Numeric Rating Scale (NRS) on fatigue were used. The evolution of the different outcomes over time was measured using mixed models. Results Of 1151 invited patients, 851 participants (67% had CD and 33% UC or IBD-U) completed one or more questionnaires (response rate 74%). Median age of the participants was 41 years, with 57% being female. No relevant changes in total scores were found over time for the IBDQ (effect estimate 0.006, 95% CI [-0.003–0.015]) and IBD-control-8 (effect estimate 0.004, 95% CI [0.998–1.011]). There was a slight, increasing trend in fatigue scores over time (effect estimate 0.011, 95% CI [0.004, 0.019]). Conclusion This first lock down due to the COVID-19 pandemic in The Netherlands did not impact on the HRQoL and disease control of patients with IBD. Up to date information may have contributed to a stable HRQoL in IBD patients even in an extreme period with restrictions and insecurities.