Background: Healthcare systems and general surgeons are being challenged by the current pandemic. The European Association for Endoscopic Surgery (EAES) aimed to evaluate surgeons’ experiences and perspectives, to identify gaps in knowledge, to record shortcomings in resources and to register research priorities. Methods: An ad hoc web-based survey of EAES members and affiliates was developed by the EAES Research Committee. The questionnaire consisted of 69 items divided into the following sections: (Ι) demographics, (II) institutional burdens and management strategies, and (III) analysis of resource, knowledge, and evidence gaps. Descriptive statistics were summarized as frequencies, medians, ranges, and interquartile ranges, as appropriate. Results: The survey took place between March 25th and April 16th with a total of 550 surgeons from 79 countries. Eighty-one percent had to postpone elective cases or suspend their practice and 35% assumed roles not related to their primary expertise. One-fourth of respondents reported having encountered abdominal pathologies in COVID-19-positive patients, most frequently acute appendicitis (47% of respondents). The effect of protective measures in surgical or endoscopic procedures on infected patients, the effect of endoscopic surgery on infected patients, and the infectivity of positive patients undergoing laparoscopic surgery were prioritized as knowledge gaps and research priorities. Conclusions: Perspectives and priorities of EAES members in the era of the pandemic are hereto summarized. Research evidence is urgently needed to effectively respond to challenges arisen from the pandemic.