Intimate Partner Violence (IPV) is a major public health problem to be addressed with innovative and interconnecting strategies for ensuring the psychophysical health of the surviving woman. According to the World Health Organization, 27% of women worldwide have experienced physical and sexual IPV in their lifetime. Most of the studies on gender-based violence focus on short-term effects, while long-term effects are often marginally included even though they represent the most serious and complex consequences. The molecular mechanisms underlying stress-related disorders in IPV victims are multiple and include dysregulation of the hypothalamic-pituitary-adrenal axis, inflammatory response, epigenetic modifications, neurotransmitter imbalances, structural changes in the brain, and oxidative stress. This review aims to explore the long-term health consequences of intimate partner violence (IPV), emphasizing the biological and psychological mechanisms underlying stress-related disorders and resilience. By integrating findings from epigenetics, microbiome research, and artificial intelligence (AI)-based data analysis, we highlight novel strategies for mitigating IPV-related trauma and improving recovery pathways. Genome-wide environment interaction studies, enhanced by AI-assisted data analysis, offer a promising public health approach for identifying factors that contribute to stress-related disorders and those that promote resilience, thus guiding more effective prevention and intervention strategies.