Introduction: Monitoring the impact of natural disasters such as pandemics on health and wellbeing is a public health priority. Stress is proven to affect pain intensity and quality of life of endometriosis patients. A cross-sectional study was conducted to determine whether the measures implemented to mitigate COVID-19 infections had a substantial impact on risk behaviors, endometriosis symptoms, stress, and access to healthcare. Methods: Electronic questionnaires that measured COVID-19 impact and peri-traumatic stress were disseminated through social media over June–September 2020 and completed by 82 adult patients with endometriosis living in Puerto Rico. Descriptive data analysis and correlations were done in quantitative data and systematic analysis of free text was done on qualitative responses. Results: Participants self-reported worsening of endometriosis symptoms and high levels of peri-traumatic stress, as well as changes in risk behaviors (exercise, nutrition, sedentarism, sleep) during the pandemic in comparison to the previous months. They also reported substantial barriers in access to medical appointments, scheduled procedures, and prescriptions. Electronic health modalities (telemedicine, mobile apps) were considered acceptable alternatives for gynecologic care during natural disasters. Conclusion: The COVID-19 pandemic negatively impacts the health and wellbeing of endometriosis patients while imposing substantial restrictions on access to health care. These timely insights will guide the development and implementation of plans to address barriers to health care and minimize long-term detrimental effects of natural disasters on the health of those living with stress-related disorders such as endometriosis.