Background Maternal socioeconomic status (SES) is closely linked to children's health outcomes. However, the marginalization-related diminished returns theory suggests that increases in SES yield smaller health gains for marginalized populations-such as Afro-Peruvian and Indigenous groups-compared to majority groups like Mestizos, largely due to systemic barriers and social disadvantage. Therefore, the current study aimed to explore ethnic disparities in the association between maternal SES on childhood anemia in Peru. Methods Using data from the 2017 to 2023 Peruvian Demographic and Health Survey, we conducted a cross-sectional study including children aged 6-59 months with their respective mothers. Ethnicity was grouped into Mestizo, Afro-Peruvian, and Indigenous (Quechua, Aimara, and native of the Amazon). Three proxies of SES were used: wealth index, level of education, and years of education. After stratifying by ethnicity, we estimated prevalence ratios (PR) with their respective 95% confidence intervals (95% CI) using generalized linear models with Poisson family. Interaction was assessed on multiplicative and additive scales. Findings Among 234,364 Peruvian mothers, 45.7% (n = 107,118) identified as Mestizo, 12.6% (n = 29,557) as Afro-Peruvian, and 41.7% (n = 97,689) as Indigenous. The overall prevalence of anemia in children was 32.2%. The association between a very rich wealth index and lower prevalence of anemia was weaker among Indigenous (PR = 0.63, 95% CI: 0.56-0.72) compared to Mestizo individuals (PR = 0.46, 95% CI: 0.42-0.50). Similarly, the association between higher maternal education and lower anemia prevalence was less pronounced for Afro-Peruvian (PR = 0.70, 95% CI: 0.62-0.79) and Indigenous groups (PR = 0.81, 95% CI: 0.77-0.86) than for Mestizos (PR = 0.63, 95%CI: 0.59-0.67). A similar pattern was noted with maternal years of education (Mestizos [PR = 0.95, 95% CI: 0.94-0.96], Afro-Peruvian [PR = 0.97, 95% CI: 0.96-0.98], and Indigenous [PR = 0.98, 95% CI: 0.98-0.99]). Interaction analysis confirmed significantly weaker associations for Afro-Peruvian and Indigenous individuals compared to Mestizos. Interpretation Maternal SES is associated with lower prevalence of childhood anemia, with stronger associations observed among Mestizo populations compared to Afro-Peruvian and Indigenous groups. This pattern aligns with the marginalization-related diminished returns theory. Maximizing SES alone does not preclude ethnic disparities but rather, may even widen them, highlighting the need for equity-focused interventions that address underlying structural and systemic barriers.