Stevia, a zero-calorie sugar substitute, is recognized as safe by the Food and Drug Administration (FDA) and the European Food Safety Authority (EFSA). In vitro and in vivo studies showed that stevia has antiglycemic action and antioxidant effects in adipose tissue and the vascular wall, reduces blood pressure levels and hepatic steatosis, stabilizes the atherosclerotic plaque, and ameliorates liver and kidney damage. The metabolism of steviol glycosides is dependent upon gut microbiota, which breaks down glycosides into steviol that can be absorbed by the host. In this review, we elucidated the effects of stevia’s consumption on the host’s gut microbiota. Due to the lack of randomized clinical trials in humans, we included in vitro using certain microbial strains and in vivo in laboratory animal studies. Results indicated that stevia consumption has a potential benefit on the microbiome’s alpha diversity. Alterations in the colonic microenvironment may depend on the amount and frequency of stevia intake, as well as on the simultaneous consumption of other dietary components. The anti-inflammatory properties of stevioside were confirmed in vitro by decreasing TNF-α, IL-1β, IL-6 synthesis and inhibiting of NF-κB transcription factor, and in vivo by inhibiting NF-κB and MAPK in laboratory animals.