Some shifts in the gut microbiota composition and its metabolic fingerprints have been associated to Sleeve gastrectomy (SG) and Roux-en-Y Gastric Bypass (RYGB). So far, plasma bile acids have been associated with post-operative glucose improvement and weight loss, but nothing is known about their metabolism in the gut lumen. As bile acids are physiologically transformed by the microbiota into various species, the aim of this work was to study how SG and RYGB-associated dysbiosis impact the bioconversion of bile acids in the intestinal lumen. Comparing SHAM (n = 9) with our validated rat models of SG (n = 5) and RYGB (n = 6), we quantified luminal bile acids along the gut and found that the metabolic transformation of bile acids (deconjugation, dehydroxylation, and epimerization) is not different from the duodenum to the colon. However, in the cecum where the biotransformation mainly takes place, we observed deep alterations of the microbiota composition, which were specific of each type of surgery. In conclusion, despite specific dysbiosis after surgery, the bile acids metabolism in the gut lumen is highly preserved, suggesting that a resilience of the gut microbiota occurs after these procedures.