Context Several therapies have been tested for combating weight gain and obesity-related metabolic diseases, and among these therapies, intermittent fasting (IF) has gained a great deal of interest. Objective The aim of this study was to provide the reader with a current survey of IF protocols and an understanding of the outcomes found to date in terms of the profile of the intestinal microbiota (IM) in obese organisms. Data Sources Data were obtained from 4 databases: PubMed, SCOPUS, LILACs, and Web of Science. Data Extraction Data from studies relating IF protocols to the microbiota and weight loss were extracted using a protocol in START program. Data Analysis Of the 82 original articles identified from the databases, 35 were eliminated due to duplication, and 32 were excluded due to not meeting the inclusion criteria. Two additional articles found in a new search were added, yielding a total of 17 studies to be included in this review. Among the protocols, alternate-day fasting (ADF) and time-restricted feeding (TRF) were the most common, and they were shown to have different mechanisms of metabolic signaling. TRF influences weight control and biochemical parameters by regulating the circadian system, and improving satiety control systems by acting on leptin secretion. On the other hand, ADF leads to a reduction of ±75% of all energy consumption regardless of dietary composition in addition to promoting hormonal adjustments that promote weight control. Furthermore, both protocols showed the ability to remodel the IM by changing the Firmicutes/Bacteroidetes ratio and increasing the abundance of strains such as Lactobacillus spp. and Akkermansia m. that have a protective effect on metabolism against the effects of weight gain. Conclusion In short, the ADF and TRF protocols have a positive effect on the remodeling of the IM and can possibly be used to control body adiposity, improve insulin sensitivity, and achieve other obesity-related metabolic changes.