Background Biological and psychological mechanisms may be responsible for menstrual irregularities occurring among women during the COVID-19 pandemic. Study design From January 2019 to September 2021, women (18- to 45-years-old and not using hormonal contraception) were recruited in Miami-Dade County, Florida. Cross-sectional, self-report surveys collected data on menstrual irregularities, COVID-19 vaccination, stress, depression, and loneliness. A EUA approved rapid test assay using whole blood measured SARS-CoV-2 IgG antibodies. Chi-square and Fisher’s exact tests described menstrual irregularities among women recruited before versus after the start of the COVID-19 pandemic and with detectable versus undetectable SARS-CoV-2 IgG antibodies. A logistic regression examined the relationship between the presence of SARS-CoV-2 IgG antibodies and menstrual irregularities controlling for age, stress, depression, and loneliness. Results Among 182 women enrolled, 73 were enrolled after pandemic onset, and 36 provided vaccination data. Having detectable SARS-CoV-2 IgG antibodies was associated with a higher percentage of menstrual irregularities among unvaccinated women (0% vs. 39%, p = .026) and among all women regardless of vaccination status (31% vs. 5%; p = .005). Adjusting for age and psychological variables, the odds of menstrual irregularities were 7.03 times (95% CI [1.39, 35.60]; p = .019) higher among women with detectable antibodies compared to women without detectable antibodies. Neither enrollment date, age, nor psychological factors were associated to menstrual irregularities. Conclusions Biological mechanisms related to SARS-CoV-2 infection may be responsible for irregular menstruation and should be further examined to mitigate the impact of the COVID-19 pandemic on women’s health.