Dietary and plasma carboxymethyl lysine (dCML, pCML) and plasma tumor necrosis factor-α (pTNF-α) may be associated with obesity in affluent society. However, evidence in women from low-middle income countries with predominantly traditional diets is lacking. We investigated the mediator effects of dCML, pCML and pTNF-α on body mass index (BMI) and waist circumference (WC) among Indonesian women. A cross-sectional study was conducted among 235 non-diabetic, non-anemic and non-smoking women aged 19–50 years from selected mountainous and coastal areas of West Sumatra and West Java. Dietary CML, pCML, pTNF-α were obtained from 2 × 24-h recalls, ultra-performance liquid chromatography-tandem mass spectrometry and enzyme-linked immunosorbent assay, respectively. Between-group differences were analyzed by the Chi-square or Mann-Whitney test and mediator effects by Structural Equation Modeling. The medians and interquartile-ranges of dCML, pCML and pTNF-α were 2.2 (1.7–3.0) mg/day, 22.2 (17.2–28.2) ng/mL and 0.68 (0.52–1.00) IU/mL, respectively, and significantly higher in the WC ≥ 80 cm than in the WC < 80 cm group, but not in BMI ≥ 25 kg/m2 compared to BMI < 25 kg/m2 group. Plasma CML and pTNF-α were positively and directly related to WC (β = 0.21 [95% CI: 0.09, 0.33] and β = 0.23 [95% CI: 0.11, 0.35], respectively). Dietary CML that correlated with dry-heat processing and cereals as the highest contributions was positively related to WC (β = 0.33 [95% CI: 0.12, 0.83]). Ethnicity, level of education, intake of fat, and intake of energy contributed to dCML, pCML and pTNF-α, and subsequently affected WC, while only ethnicity contributed to BMI through dCML, pCML and pTNF-α (β = 0.07 [95% CI: 0.01, 0.14]). A positive direct effect of dCML on pCML and of pCML and pTNF-α on WC was seen among Indonesian women. Dietary CML seems to have several paths that indirectly influence the increases in WC if compared to BMI. Thus, intake of CML-rich foods should be reduced, or the foods consumed in moderate amounts to avoid the risk of central obesity in this population.