Gut microbiota dysbiosis and endocrine dysregulation are key players in metabolic dysfunction-associated steatotic liver disease (MASLD) development. This study evaluated whether advanced microbiome therapeutics can restore intestinal microbial equilibrium and gut-liver axis balance during MASLD recovery. MASLD was induced in mice using a high-fat, high-sugar diet, and then shifted to a standard diet, where intervention groups received engineered Escherichia coli Nissle 1917 expressing IGF1 (EcNI) or aldafermin (EcNA), and control groups received E. coli Nissle 1917 vehicle (EcN) or no microbial intervention (CTRL). EcNI and EcNA improved MASLD recovery compared to controls by lowering hepatic fat, plasma cholesterol, and body weight, while increasing bacterial diversity, plasma acetate, and propionate, and modulating particular microbial groups, potentially alleviating dysbiosis. Additionally, EcNI and EcNA downregulated acetyl-CoA, the steroid hormone biosynthesis pathway, and EcNA upregulated the pentose phosphate pathway and pyruvate, which are related to oxidative stress reduction. These results suggest that EcNI and EcNA are potential novel treatments for MASLD.