Youth-onset type 2 diabetes mellitus (T2DM) has an aggressive clinical course and is usually preceded by obesity and metabolic syndrome (MetS). Lipids have emerged as potential biomarkers for studying metabolic risk factors and predicting disease progression. An untargeted lipidomic analysis by liquid chromatography-mass spectrometry was performed in thirty pediatric subjects with T2DM and MetS and a healthy group. Plasma lipids were associated with obesity, metabolic risk factors, inflammatory biomarkers, and gut microbiota. A total of 375 lipid species were annotated. MetS and T2DM groups had increased levels of phosphocholines (15-18), phosphoinositols (2-3), sphingomyelins (2-3), and triglycerides (1-4), and lower plasmalogens (2-6) and lysophospholipids (1-2). Phosphocholines, phosphoinositols, sphingomyelins, and triglycerides positively correlated with metabolic risk factors such as body mass index (BMI), waist and hip circumference, triglycerides, glucose, insulin, and HOMA-IR. Ceramides were significantly higher in MetS and T2DM in regression analysis, adjusted for BMI, age, and sex, and only increased with higher BMI in the healthy group. Significant positive correlations were observed for phosphocholines and phosphoinositols with species from the phyla Pseudomonadota and Bacillota, like Weissella cibaria and Enterobacter hormaechei, and the latter species with ceramides. This study provides novel evidence on the role of plasma lipids in the pathophysiology of MetS and T2DM in children and adolescents and their associations with gut microbial species. These findings documented opportunities for developing therapeutic strategies, such as dietary interventions and microbiome modulation, to mitigate the burden of metabolic diseases in pediatric populations.