Objective: Determine the association between intimate partner violence against Peruvian women and adequate regulation of the emotions and behaviors of children between 24 and 59 months old. Methods: This cross-sectional study analyzed secondary data obtained from the ENDES-2019. The dependent variable was the regulation of emotions and behaviors in 24 to 59-month-old children. The independent variable was partner violence (physical, sexual, verbal or psychological) against mothers at some point in their life. Prevalence ratios (PR) were calculated and adjusted with their 95% confidence interval (CI) to evaluate the association between intimate partner violence and adequate regulation of emotions and behaviors. Results: Data from 8,473, 15 to 49-year-old mothers and their children aged 24 to 59 months were analyzed. Intimate partner violence was reported by 57.1% of the women, and 31.6% of the children showed adequate regulation of emotions and behaviors. The probability of children of mothers who were victims of intimate partner violence adequately regulating their emotions and behaviors was low (aPR = 0.81, 95% CI: 0.75–0.88), with an aPR = 0.82 (95% CI: 0.76–0.89) and an aPR = 0.84 (95% CI: 0.76–0.93) for those with mothers suffering psychological or physical violence, respectively, with no differences in children of mothers suffering sexual violence by their partner. Conclusions: Six out of 10 Peruvian women have suffered partner violence at some point in their life, and only three out of 10 children between 24 and 59 months old adequately regulate their emotions and behaviors. Children of mothers suffering physical and verbal or psychological violence by their partners were less likely to regulate their emotions and behaviors adequately.