This study compared the current nutritional status, hemoglobin levels and their associations with soil-transmitted helminth (STH) infections between two categories of Negritos (indigenous): (i) Inland Jungle Villages (IJV) (ii) and Resettlement Plan Scheme (RPS) near town peripheries, decades after redevelopment and demarginalization. A total of 416 Negritos (IJV: 149; RPS: 267) was included for nutritional profiling based on anthropometric analysis. However, only 196 (IJV: 64; RPS: 132) individuals consented to blood taking for the hemoglobin (Hb) measurements. Subsequently, the association of undernutrition and anemia with STH infections were determined based on univariate and multivariate logistic regression analyses. The overall prevalence of stunting, wasting, and underweight amongst children and adolescents (n = 343) were 45.8%, 42.3% and 59.1%, respectively. In adults (n = 73), the prevalence of underweight was low (6.8%) but overweight and obese was prominent (26.0%). For anemia (n = 196), an overall prevalence rate of 68.4% were observed with 80% and 70.4% of children aged 2–6 y/o and aged 7–12 y/o, respectively being anemic. Comparatively, the prevalence of underweight (WAZ) was significantly higher in the RPS versus the IJV (P = 0.03) In the IJV, children aged ≤ 6 y/o and having STH poly-parasitism were associated with underweight (P = 0.01) and moderate-severe T. trichiura infection was associated with anemia. Whilst in the RPS, underweight was highly associated with only T. trichiura infection (P = 0.04). Wasting was significantly associated with young children aged ≤10 in both IJV (P = 0.004) and RPS (P = 0.02). Despite efforts in improving provision of facilities and amenities among the indigenous, this study highlighted a high magnitude of nutritional issues among the Negritos especially those in the RPS and their likely association with STH infections and decades of demarginalization. Joint nutritional intervention strategies with mass anti-helminthic treatment are imperative and urgently needed to reduce the undernutrition problems especially among indigenous children.