To examine the rates and factors associated with alcohol consumption after the recognition of pregnancy among indigenous pregnant women, as well as the rates and factors associated with continuing alcohol consumption after the recognition of pregnancy among indigenous pregnant women who drank alcohol before the recognition of pregnancy in 10 hospitals in southern and eastern Taiwan. A total of 806 indigenous women who had just given birth in 10 hospitals in southern and eastern Taiwan were recruited. They were interviewed to collect their substance use information, demographic characteristics, psychological health status, history of physical abuse, and pregnancy history. The rates of alcohol consumption after the recognition of pregnancy in all indigenous pregnant women and the rates of continuing alcohol consumption after the recognition of pregnancy among those who drank alcohol before the recognition of pregnancy were calculated. The factors relating to alcohol consumption and continuing alcohol consumption after the recognition of pregnancy were examined using logistic regression analyses. The results of this study found that 26.6% of indigenous pregnant women drank alcohol at any stage after the recognition of pregnancy, and 52.5% of indigenous pregnant women who drank alcohol before the recognition of pregnancy persisted in drinking alcohol after the recognition of pregnancy. Multiple parities, smoking or chewing betel quid after the recognition of pregnancy, and a higher frequency of drinking alcohol before the recognition of pregnancy were significantly associated with alcohol consumption and continuing alcohol consumption after the recognition of pregnancy. Meanwhile, being single or divorced, and intimate partner violence after the recognition of pregnancy were significantly associated with alcohol consumption after the recognition of pregnancy. High prevalence rates of alcohol consumption and continuing alcohol consumption after the recognition of pregnancy were found among indigenous pregnant women in Taiwan. Early detection of alcohol consumption and effective intervention for alcohol consumption during pregnancy are needed.