Introduction: Increased reporting of menstrual disturbances post-vaccination and inadequate inclusion of questions about menstruation in vaccine trials and disease progression studies have been the baseline for conducting this study. We aim to assess the influence of vaccines and COVID-19 infection on menstruation and identify patterns, if any, in cycles post-disease/vaccination. Methods: A multicenter observational study was performed using a questionnaire-based survey via an online link. The participants who filled the survey were predominantly in the age group of 21–25 years (80%). Participants with prior menstrual irregularities were eliminated from the study. Results: The prevalence of unusual menstrual cycles post-infection/vaccination was 21.7%. A total of 17.11% experienced changes post-vaccination and 22.8% of the infected individuals reported abnormalities post-COVID-19 disease. A substantial increase in dysmenorrhea was reported (p <0.001) post-infection/vaccination. An increase in menstrual flow was observed in 14.9% post-vaccination and 23.9% post-infection. Conclusion: Menstrual changes post-vaccination were insignificant; however, significant differences in menstruation were reported post-infection. The study strengthens the association between COVID-19 and menstruation and urges the inclusion of menstrual health in disease intervention studies.