Background: Traumatic events, including child abuse and intimate partner violence, are highly prevalent among women of child-bearing age. These traumatic experiences may impact maternal and offspring physical and mental health. A proposed mechanism for these effects is maternal hypothalamic-pituitary-adrenal (HPA) axis dysregulation which can be measured using hair corticosteroid levels. Aims: This study aims to examine the association of child abuse and intimate partner violence exposure with HPA axis functioning, as measured by hair corticosteroid levels in a cohort of pregnant women. Methods: We included data from 1822 pregnant women (mean gestational age 17 weeks) attending a prenatal clinic in Lima, Peru. We extracted cortisol and cortisone concentrations from hair samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Each participant provided 6-cm hair samples: 3 cm hair segment closest to the scalp reflecting HCC in early pregnancy (first three months), and 3–6 cm from the scalp reflecting HCC in pre-pregnancy (three months prior to conception). Multivariable linear regression procedures were used to assess the association between maternal trauma exposure and hair corticosteroid levels. Results: Overall, women who experienced child abuse on average had higher levels of cortisol (p < 0.01) and cortisone (p < 0.0001) after adjustment for age, race, adult access to basic foods and hair treatments. For the hair segment reflecting early pregnancy, presence of child abuse was associated with a 0.120 log unit increase in cortisol and a 0.260 log unit increase in cortisone (p < 0.001). For the hair segment reflecting pre-pregnancy, a history of child abuse was associated with a 0.100 log unit increase in cortisol and a 0.180 log unit increase in cortisone (p < 0.01). Results also suggested an impact of intimate partner violence on HPA regulation; however, associations were not statistically significant after controlling for child abuse. Conclusions: These results underscore the long-lasting impacts of exposure to adversity and trauma during early life. Our study findings will have implications for research investigating HPA axis function and long-term effects of violence on corticosteroid regulation.