Bariatric surgery is currently the recommended therapy for significant weight reduction and remission of type 2 diabetes. Different types of bariatric surgery result in dramatic changes to gut bacteria but the contribution of such changes to the metabolic benefits achieved is still unclear. This systematic review of 14 clinical studies, incorporating 222 participants (146 patients with Roux-en-Y gastric bypass, 25 with sleeve gastrectomy, 30 with biliointestinal bypass, 7 with vertical banded gastroplasty, and 14 with an adjustable gastric band) reveals generally increased microbial diversity and gene richness after surgery. Major species-level changes include a decrease in the relative abundance of Faecalibacterium prausnitzii and increase in Escherichia coli. Decreases in the relative abundance of Firmicutes after sleeve gastrectomy and increases in Bacteroidetes and Proteobacteria after Roux-en-Y gastric bypass were seen. Microbial changes after surgery are discussed in the context of potential confounding effects of baseline diet, medications, and type 2 diabetes, with recommendations to consider these factors in future studies, to identify potentially causal associations with observed metabolic benefits.