We aimed to describe and characterize the gut microbiota composition and diversity in children with obesity according to their metabolic health status. Anthropometry, Triglycerides, HDL cholesterol, HOMA-IR, and systolic and diastolic blood pressure (SBP, DBP) were evaluated (and z-score calculated) and faecal samples were collected from 191 children with obesity aged from 8 to 14. All children were classified depending on their cardiometabolic status in either a “metabolically healthy” (MHO; n = 106) or “metabolically unhealthy” (MUO; n = 85) group. Differences in gut microbiota taxonomies and diversity between groups (MUO vs MHO) were analysed. Alpha diversity index was calculated as Chao1 and Simpson’s index, and β-diversity was calculated as Adonis Bray–Curtis index. Spearman’s correlations and logistic regressions were performed to study the association between cardiometabolic health and the microbiota. Children in the MUO presented significantly lower alpha diversity and richness than those in the MHO group (Chao1 index p = 0.021, Simpson’s index p = 0.045, respectively), whereas microbiota β-diversity did not differ by the cardiometabolic health status (Adonis Bray–Curtis, R2 = 0.006; p = 0.155). The MUO group was characterized by lower relative abundances of the genera Christensenellaceae R7 group (MHO:1.42% 0.21–2.94; MUO:0.47% 0.02–1.60, p < 0.004), and Akkermansia (MHO:0.26% 0.01–2.19; MUO:0.01% 0.00–0.36, p < 0.001) and higher relative abundances of Bacteroides (MHO:10.6% 4.64–18.5; MUO:17.0% 7.18–27.4, p = 0.012) genus. After the adjustment by sex, age, and BMI, higher Akkermansia (OR: 0.86, CI: 0.75–0.97; p = 0.033), Christensenellaceae R7 group (OR: 0.86, 95% CI: 075–0.98; p = 0.031) and Chao1 index (OR: 0.86, CI: 0.96–1.00; p = 0.023) represented a lower risk of the presence of one or more altered cardiovascular risk factors. Lower proportions of Christensenellaceae and Akkermansia and lower diversity and richness seem to be indicators of a metabolic unhealthy status in children with obesity.