Obesity is associated with chronic inflammation, intestinal dysbiosis, and colorectal cancer risk. The anti-cancer effects of kefir are highlighted. Here, lactating Wistar rats were divided into: Normal litter (NL); Kefir normal litter (KNL); Small litter (SL); Kefir small litter (KSL). The NL and SL groups received 1 mL of water/day; KNL and KSL received kefir milk daily (108 CFU/mL) during lactation. After weaning, the pups continued to receive the same treatments until 60 days. At 67 days old, colorectal carcinogenesis was induced through intraperitoneal injection of 1,2-dimethylhydrazine. At 240 days, visceral adipose tissue was higher in SL compared to NL, KNL, and KSL. Kefir intake was found to suppress the number of tumors in both KNL and KSL groups (-100% and -71.43%; p < 0.01, respectively). IL-1β, IL-6, TNF-α, and NO levels in the colon were higher in the NL and SL compared to the KNL and KSL. The gut microbiota in cecal samples of SL was enriched with Alloprevotella, Acinetobacter, and Bacteroides. In contrast, the cecal contents of KSL and KNL were higher Romboutsia. Thus, neonatal overfeeding leads to greater adiposity, inflammation and number of colon tumors in adulthood. Early-life nutrition based on kefir reverted these alterations.