Introduction: Obesity in Indonesia reached 36.8% in 2023, a condition linked to elevated levels of Interleukin-6 (IL-6) and impaired cell integrity, as measured by phase angle. Omega-3 fatty acids are nutrients known to reduce IL-6; however, intake among individuals with obesity remains low. This study aimed to assess the relationships among dietary omega-3 fatty acid intake, plasma IL-6 levels, and bioimpedance phase angle (PhA) in obese Indonesian adults. Methods: In this cross-sectional study, 88 obese (BMI ≥ 25 kg/m²) men and women aged 19– 59 years were recruited at Universitas Indonesia Hospital. Omega-3 fatty acid intake was quantified via a Semi-Quantitative Food Frequency Questionnaire (SQ-FFQ) and NutriSurvey. PhA was measured by bioelectrical impedance analysis (SECA mBCA 515), and IL-6 by ELISA. Spearman’s rank correlation assessed bivariate associations; multivariate linear regression identified independent predictors of PhA. results: Omega-3 fatty acid intake correlated weakly and positively with PhA (r = 0.24, p = 0.026) but not with IL-6 (r = −0.12, p = 0.265). IL-6 correlated inversely with PhA (r = −0.29, p = 0.007). In regression, male sex and higher energy intake independently predicted greater PhA; omega-3 fatty acid and IL-6 were non-significant. Results: Omega-3 fatty acid intake correlated weakly and positively with PhA (r = 0.24, p = 0.026) but not with IL-6 (r = −0.12, p = 0.265). IL-6 correlated inversely with PhA (r = −0.29, p = 0.007). In regression, male sex and higher energy intake independently predicted greater PhA; omega-3 fatty acids and IL-6 were non-significant. Discussion: These results add to the accumulating evidence that omega-3 fatty acids can affect cellular health, as indicated by PhA, more than lowering systemic inflammation directly. This supports the need to pay attention to PhA as a prospective marker for dietary and metabolic health interventions in the treatment of obesity. Further, the finding of an inverse correlation between IL-6 and PhA indicates that inflammation can worsen muscle integrity and strengthen the need to treat inflammation in obesity. Conclusion: Low omega-3 fatty acid intake and higher IL-6 are associated with reduced cellular integrity (lower PhA) in obesity; PhA is influenced more by sex and caloric intake than by omega-3 fatty acid alone.