We aim to review the available literature on obese patients treated with bariatric procedures, in order to assess their effect on the metabolic and gut microbiota profiles. A systematic literature search was performed in PubMed, Cochrane library, and Scopus databases, in accordance with the PRISMA guidelines. Twenty-two studies (562 patients) met the inclusion criteria. This study points to significant amelioration of postoperative levels of glucose, insulin, triglycerides, total cholesterol, LDL, HDL, HOMA-IR, food intake, and diabetes remission. Branched-chain amino acids (BCAAs) decreased, while trimethylamine-n-oxide (TMAO); glucagon-like peptide 1, 2 (GLP-1, GLP-2); and peptide YY (PYY) increased postoperatively. Postoperative gut microbiota was similar to that of lean and less obese objects. Well-designed randomized trials are necessary to further assess the host metabolic-microbial cross-talk after bariatric procedures.