Background: It has been reported that coronavirus disease 2019 (COVID-19) vaccines could provoke flu-like symptoms and changes in menstrual cycles in some women, probably as a result of the immune response caused by the vaccination itself. Altered local immunity and inflammatory processes are found in women suffering from adenomyosis and endometriosis, this having a role in the typical symptomatic manifestations. This study aims to investigate the prevalence of side effects like abnormal uterine bleeding (AUB) or pain following the administration of COVID-19 vaccines in women with adenomyosis or endometriosis. Methods: A retrospective cohort study was performed on 172 patients referring to our Chronic Pelvic Pain Center, who underwent COVID-19 vaccination. A hystorical cohort of sixty-three non-vaccinated women was used as control. We collected anamnestic data and each woman scored menstrual pain, chronic pelvic pain, and the occurrence of AUB before and after vaccination. Results: Among control women, no one showed AUB, and only 2 women experienced a slight worsening of menstrual pain. Side effects were observed in 29/172 (16.8%) of COVID-19 vaccinated women, independent of whether they were on hormone therapy. In comparison to asymptomatic, symptomatic women had a higher prevalence of adenomyosis (82.7% vs 63.6%), adenomyosis being present in 100% of the 6 women with intermenstrual bleeding, in 79% of the 19 women with heavy menstrual bleeding and in 81% of the 16 women with pain worsening. Nine out of 55 (16.3%) women with endometrioma experienced side effects. Among these, the 3 women that were not on hormone therapy experienced a huge increase in endometrioma volume from +208% to +806%. In one case emergency surgery was necessary for endometrioma rupture and hemoperitoneum. Conclusions: In our sample, adenomyosis appears strictly related to the manifestation of post-vaccine side effects. Hormone therapy seems to be insufficient to protect from post-vaccine symptoms, but the increase in endometrioma volume was observed only in cases without hormone therapy.