Cranberry consumption has been demonstrated to improve features of the metabolic syndrome, therefore providing an alternative strategy to prevent obesity and type-2 diabetes. Moreover, gut dysbiosis is now considered as a key factor in metabolic disorders. In order to understand the involvement of phenolic compounds in the health-improving effects of cranberry, this study aimed to investigate their bioavailability after oral administration of a cranberry extract (CE) to high-fat high-sucrose (HFHS) fed mice, and to explore a possible modulation of gut microbiota composition following a co-supplementation with spores of Bacillus subtilis CU1 probiotic (CE/P). Phenolic metabolites were extracted and characterized from plasma using μSPE-UHPLC-MS/MS, and a metagenomic analysis was performed on feces to assess gut bacterial composition. 22 circulating metabolites were identified, mainly microbial degradation products of native cranberry phenolic compounds. Plasma concentration of 3 microbial metabolites was significantly increased with the CE/P co-treatment: p-coumaric acid, m-coumaric acid and p-hydroxybenzoic acid (+53%, +103% and +70%, respectively). Associated to this modulation, we reported significant differences in the proportion of Barnesiella and Oscillibacter genera in CE/P treated mice in comparison with control animals. This study thus highlights the impact of an altered gut microbiota on phenolic compounds degradation and bioavailability in mice.