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The role of <i>Bifidobacterium</i> species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied in recent years. This paper discusses the discovery of signature biomarkers for obesity and T1D based on data from a novel test for profiling several <i>Bifidobacterium</i> species, combined with metabolomic analysis. Through the NUTRISHIELD clinical study, a total of 98 children were recruited: 40 healthy controls, 40 type 1 diabetics, and 18 obese children. <i>Bifidobacterium</i> profiles were assessed in stool samples through an innovative test allowing high taxonomic resolution and precise quantification, while SCFAs and branched amino acids were measured in urine samples through gas chromatography–mass spectrometry (GC-MS). KIDMED questionnaires were used to evaluate the children’s dietary habits and correlate them with the <i>Bifidobacterium</i> and metabolomic profiles. We found that <i>B. longum</i> subs. <i>infantis</i> and <i>B. breve</i> were higher in individuals with obesity, while <i>B. bifidum</i> and <i>B. longum</i> subs. <i>longum</i> were lower compared to healthy individuals. In individuals with T1D, alterations were found at the metabolic level, with an overall increase in the level of the most measured metabolites. The high taxonomic resolution of the <i>Bifidobacterium</i> test used meant strong correlations between the concentrations of valine and isoleucine, and the relative abundance of some <i>Bifidobacterium</i> species such as <i>B. longum</i> subs. <i>infantis</i>, <b>B. breve</b>, and <i>B. bifidum</i> could be observed.