Childhood is a critical stage of development during which diet can have profound influence on the microbiota–host interactions, leading to potentially lifelong impacts. This study aimed to investigate whether the consumption of cafeteria diet (CAFD) and sugary drinks during early rat life alters the structure of the gut microbial community and the metabolic activity. Four-week-old male Wistar rats (n = 27) were fed a standard chow diet with ad libitum access to water (CD) or to sucrose solution (HSD), and a third group was fed with CAFD and a sucrose solution for 14 weeks. HSD and CAFD consumption induced alterations in Firmicutes to Bacteroidetes ratio, Proteobacteria, and Verrucomicrobia. HSD increased the abundance of Barnesiella, whereas CAFD induced a depletion of Saccharibacteria. CAFD increased total white adipose tissue (WAT) weight (p < 0.0005) compared to CD. When CAFD was compared to HSD, a significant difference was found only for retroperitoneal WAT (p < 0.0005). Unhealthy diet-fed groups presented higher glucose (p < 0.0005), total cholesterol and creatinine serum levels (p < 0.005) compared to the CD rats. Early-life consumption of HSD, and of CAFD even more so, can have long-lasting negative effects on metabolic function. The gut microbiota communities were distinctively perturbed by diet composition.