Abstract Background: Continuous monitoring and early detection of placental changes through imaging and Doppler studies can help in managing and improving pregnancy outcomes in malaria-endemic regions such as Nigeria. The aim of this study is to investigate the impact of malaria on placental velocimetry in the second and third trimester, among pregnant women in Onitsha metropolis. Materials and Methods: The study design was a case control carried among pregnant women with malaria and comparing with apparently health controls. Both groups undergo laboratory test for malaria and Doppler ultrasound scan for placental pulsatile index and resistive index using standard protocols. Descriptive and inferential statistical tools were used for statistical analysis with level of statistical significance set at p < 0.005. Results: The PI differs significantly between pregnancies affected by malaria and healthy controls, with a small to moderate effect size (F(1, 396) = 11.831, p < 0.001, partial η² = 0.029). The RI does not significantly differ between the second and third trimesters (F (1, 396) = 1.016, p = 0.31, partial η² = 0.003), the effect of malaria on RI does not vary across trimesters F (1, 396) = 1.656, p = 0.19, partial η² = 0.004). Conclusion: The PI differs significantly between pregnancies affected by malaria and healthy controls, with a small to moderate effect size, suggesting some practical relevance. There was no statistically significant main effect of trimester, indicating that PI does not differ between the second and third trimesters. Importantly, the interaction effect between malaria status and trimester was statistically significant. This suggests that the effect of malaria on PI varies depending on the trimester. The RI differs significantly between pregnancies affected by malaria and healthy controls, although the effect size was small. However, there was no statistically significant main effect of trimester and RI does not significantly differ between the second and third trimesters.