Introduction The reorganization of the healthcare system prompted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed unique challenges for Residency Training Programs worldwide. To mitigate its potential negative effects, it is crucial to assess how the pandemic influenced the activity and quality of life of residents. The purpose of this study was to assess the impact of the pandemic on residents’ competencies, satisfaction, working load, training patterns and occupational exposure in the clinical, surgical, research and didactic fields and to quantify its effects on quality of life and risk perception. Methods An online cross-sectional survey was distributed between 1 June 2020 and 31 July 2020 to 1645 residents enrolled in all Residency Programs of four Universities in northern Italy. The survey included questions about clinical, surgical, and research competencies, educational activity, and quality of life pre- and post-pandemic, and on policies and workplace interventions to reduce exposure to SARS-CoV-2. The main outcome measure was the variation in self-perceived clinical, surgical and research competencies and in specialistic training. Data were analysed using the statistical package R Core Team 4.0.0, estimating mean and standard deviation or median and interquartile range for continuous variables. Variables were compared using chi-square test, Fisher exact tests or McNemar test, as appropriate. A multivariate binary logistic regression analysis was performed to test the effect of different factors on the impact of coronavirus disease-2019 (COVID-19) on self-perceived clinical and research competencies and on didactic training. Results A total of 498 residents completed the survey (response rate 30.3%). The mean age of respondents was 28.9 years, 62.9% were women, and 52.4% were enrolled in the first two years of Training Programs. On the first pandemic wave, over 60% of residents reported a negative impact of the pandemic on their specialistic training. In contrast, 40% of residents involved in clinical duties perceived an improvement in their clinical competences, especially those involved in COVID-19 care, and 34.5% perceived an improvement in their research competences, particularly junior residents, while only 3.5% reported an improvement in surgical skills. Most surgical residents (88.5%) reported a decrease in surgical activities, mainly due to reduced hospital bed capacity and reduction of elective surgery. Almost 90% of all residents experienced a reduction in their didactic activities, but 80% stated their Residency Program adopted virtual training methods. A statistically significant reduction in all examined quality of life items post-pandemic vs. pre-pandemic was found. Even though most survey participants reported the availability of personal protective equipment for residents, 44% considered themselves to be at higher risk of exposure compared to senior staff. Conclusion COVID-19 pandemic caused a significant disruption in surgical training, but it had a positive impact on clinical competencies among residents involved in COVID-19 and urgent care. The pandemic had a detrimental effect on all quality of life aspects, and most residents considered themselves at higher risk of SARS-CoV-2 infection compared to other healthcare professionals. Key Messages Coronavirus disease-2019 (COVID-19) pandemic caused a significant disruption in surgical training, but it had a positive impact on clinical competencies among residents involved in COVID-19 and urgent care. Most residents experienced a reduction of didactic activities. Although the majority of training programs implemented virtual training methods to counteract the restrictions imposed by the pandemic, only half of the residents were satisfied of them. A vast proportion of residents had a high occupational exposure to SARS-CoV-2 and considered themselves at higher risk of COVID-19 infection compared to senior staff. The survey highlighted a statistically significant reduction in five key quality of life measures (i.e. sleep, mood, familiar relationships and social relationships quality and employment satisfaction) during the first wave, with mood and social relationships being the most affected. Notably, employment satisfaction was significantly higher in medical compared to surgical residents.