Background: One in four South African women will experience intimate partner violence (IPV) in their lifetime, potentially increasing their biological stress. In South Africa, limited IPV and stress research has utilized multiple timepoints or examined modifying factors. Cash transfers (CTs) are associated with reduced IPV and stress and may be an intervention target. Aims: We used data-driven methods to identify longitudinal IPV trajectory groups among South African adolescent girls and young women (AGYW), estimate each group's association with stress, and assess modification by a CT. Methods: A total of 2,183 South African AGYW ages 13 to 24 years from the HIV Prevention Trials Network 068 study were randomized to a CT or control group. Physical IPV was measured five times (2011-2017), and stress was captured once (2018-2019). Stress measures included the Cohen Stress Scale and stress biomarkers (C-reactive protein (CRP), cytomegalovirus (CMV), herpes simplex virus type-1 (HSV-1)). Group-based trajectory modeling identified IPV trajectories; ordinal logistic regression estimated the association between trajectory group and stress. Results: A two-group quadratic trajectory model was identified (higher trajectory group = 26.7% of AGYW; lower trajectory group = 73.3%). In both groups, the probability of IPV increased from ages 13 to 17 years before declining in early adulthood. However, the higher group's probability peaked later and declined gradually. The higher trajectory group was associated with an increased odds of elevated CRP (OR: 1.41, 95% CI [1.11, 1.80]), but not with other stress measures. The CT modified the relationship with CMV: a positive association was observed among the usual care arm (OR: 1.59, 95% CI [1.11, 2.28]) but not the CT arm (OR: 0.85, 95% CI [0.61, 1.19]). Conclusions: Sustained IPV risk during adolescence was associated with elevated CRP in young adulthood. The relationship between IPV and elevated CMV was attenuated among those receiving a CT, suggesting that CTs could possibly reduce biological stress due to IPV.