Background: Globally, there is evidence supporting the co-occurrence of intimate partner violence (IPV), substance use disorders (SUD) and mental health disorders among women in prisons, however, there is limited research investigating these domains in the Andean region where rates of female incarceration have increased. The study objective was to explore the prevalence of IPV, SUD and depression among incarcerated women in a Peruvian prison and explore associations among these variables and related correlates. Methods: 249 incarcerated women responded to a questionnaire about IPV, substance use, depression, and sexual behavior, and were screened for HIV/sexually transmitted diseases (STDs). Univariate analysis and logistic regression were used to estimate relative risk and the influence of substance use and depression on IPV rates. Results: Twelve months prior to incarceration, of the women with sexual partners pre-incarceration (n = 212), 69.3% experienced threats of violence, 61.4% experienced ≥1 acts of physical violence, and 28.3% reported ≥1 act of sexual aggression. Pre-incarceration, 68.1% of drug-using women had a SUD, and 61.7% of those who consumed alcohol reported hazardous/harmful drinking. There were 20 (8.0%) HIV/STD cases; and 67.5% of the women reported depressive symptoms. Compared to women with no experiences of physical violence, a greater proportion of women who experienced least l violent act had depressive symptoms and engaged in sex work pre-incarceration. Depression was associated with physical violence (adjusted relative risk = 1.35, 95% confidence interval: 1.14–1.58). Recommendations: The findings provide evidence of a syndemic of IPV, substance abuse and depression among incarcerated women in a Peruvian prison. To help guide policy makers, further research is needed to determine if this is indicative of trends for other at-risk women in the region, and viable options to treat these women during incarceration to prevent recidivism and other long-term negative sequalae.