Intermittent fasting (IF) is an emerging dietetic intervention that has been associated with improved metabolic parameters. Nowadays, the most common IF protocols are Alternate-Day Fasting (ADF) and Time-Restricted Fasting (TRF), but in this review and meta-analysis we have also considered Religious Fasting (RF), which is similar to TRF but against the circadian rhythm. The available studies usually include the analysis of a single specific IF protocol on different metabolic outcomes. Herein, we decided to go further and to conduct a systematic review and meta-analysis on the advantages of different IF protocols for metabolic homeostasis in individuals with different metabolic status, such as with obesity, diabetes mellitus type 2 (T2D) and metabolic syndrome (MetS). Systematic searches (PubMed, Scopus, Trip Database, Web of Knowledge and Embase, published before June 2022) of original articles in peer-review scientific journals focusing on IF and body composition outcomes were performed. Sixty-four reports met the eligibility criteria for the qualitative analysis and forty-seven for the quantitative analysis. Herein, we showed that ADF protocols promoted the major beneficial effects in the improvement of dysregulated metabolic conditions in comparison with TRF and RF protocols. Furthermore, obese and MetS individuals are the most benefited with the introduction of these interventions, through the improvement of adiposity, lipid homeostasis and blood pressure. For T2D individuals, IF impact was more limited, but associated with their major metabolic dysfunctions—insulin homeostasis. Importantly, through the integrated analysis of distinct metabolic-related diseases, we showed that IF seems to differently impact metabolic homeostasis depending on an individual’s basal health status and type of metabolic disease.