There is limited information about the effects of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection during the first trimester of pregnancy on the risk of major congenital malformations (MCMs). The International Registry of Coronavirus Exposure in Pregnancy (IRCEP) was designed to estimate the relative risk of adverse perinatal outcomes among women with Coronavirus Disease 2019 (COVID‐19) at specific times during gestation. Adult women were eligible to enroll if they had a SARS‐CoV‐2 test, regardless of the results, or clinically confirmed COVID‐19 during pregnancy. Self‐administered questionnaires collected data on SARS‐CoV‐2 infection, pregnancy outcomes (including detailed questions on MCMs), and potential confounders. The analysis of MCMs includes women with either a positive SARS‐CoV‐2 PCR test or a clinical diagnosis of COVID‐19 during the first trimester (exposed group) or a negative SARS‐CoV‐2 test (reference) that enrolled while pregnant. Sensitivity analyses were restricted to participants who enrolled before the availability of informative prenatal screening tests and extended to those enrolled after end of pregnancy. Generalized linear models were used to estimate relative risks (RR) and 95% confidence intervals (CI). Of 17,163 participants enrolled between June 2020 and July 2021, 1727 had a SARS‐CoV‐2 infection during the first trimester, of whom 1,675 enrolled during pregnancy. Of 10,235 controls with a negative test during pregnancy, 4,172 enrolled during pregnancy. Restriction to participants with complete follow‐up reduced the sample size to 92 exposed and 292 unexposed reference pregnancies. MCMs were reported in 3 (3.3%) exposed and 8 (2.7%) unexposed (RR 1.2; 95% CI 0.32–4.2) newborns. The RR was 2.5 (95%CI 0.23–27) among those enrolled before prenatal screening, and 2.2 (95%CI 0.89–5.3) in the overall study population including those enrolled post‐pregnancy. No specific pattern of malformations was observed. Although results are compatible with no major teratogenic effects associated with maternal SARS‐CoV‐2 infection, RR estimates were imprecise and larger studies are warranted.