The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with gastrointestinal disease who needed to undergo endoscopic procedures. In the second year of the COVID-19 pandemic, due to restrictions for elective endoscopic procedures, a large number of cancer patients were prevented from early diagnosis of several digestive cancers, which has led to a serious burden in the health system that now needs to be dealt with. We designed a prospective study that included patients in whom access to elective endoscopic examinations during the COVID-19 pandemic had been delayed. Our aim was to investigate the impact of the COVID-19 pandemic on the diagnosis rate of digestive tract malignancies in the context of health crisis management that generates an ethical dilemma regarding the balance of utilitarianism versus deontology. Our study shows that the decrease in the number of newly diagnosed gastrointestinal cancers by endoscopy and biopsy during the pandemic restrictions and the delay in diagnosis have had a clear impact on stage migration due to disease progression.