Understanding the human gut microbiota is key to assessing dietary impacts on health. This work combines a narrative review with a metagenomic analysis of 1000 gut samples to evaluate how honey influences microbial communities. The analysis confirms that Firmicutes and Bacteroidota dominate the gut microbiota, followed by Actinobacteria and Proteobacteria. Microbial diversity is established early in life and is shaped by factors such as birth mode and diet, with colonization beginning before birth. Our analysis confirms that microbial colonization starts in utero and continues after birth, with distinct compositions observed between vaginal and cesarean deliveries. Focusing on honey, our results show that it creates a distinct microbial signature characterized by the enrichment of beneficial genera such as Lactobacillus, Bifidobacterium, Megamonas, and Streptococcus and the suppression of pathogenic species like Escherichia coli, Clostridium, Staphylococcus, and Proteus. Honey’s effect is attributed to its bioactive compounds—particularly oligosaccharides and polyphenols—which promote beneficial bacteria and inhibit pathogens. Notably, polyphenols reach the lower gastrointestinal tract and exhibit stronger modulation than that of fructo-oligosaccharides alone. Therapeutically, honey has shown promise not only in adults but also in vulnerable populations like preterm infants, where it enhances the colonic microbiota when combined with infant formula. These findings suggest that honey is more than a natural sweetener—it acts as a functional food with microbiota-targeted benefits, supporting its inclusion in dietary interventions for gut health restoration.