Purpose: To conduct a systematic review and multilevel meta-analysis of the current literature as to the effects of interval training (IT) vs moderate intensity continuous training (MICT) on measures of body composition, both on a whole-body and regional level. Methods: We searched English-language papers on PubMed/MEDLINE, Scopus, CINAHL, and sportrxiv for the following inclusion criteria: (a) randomized controlled trials that directly compared IT vs MICT body composition using a validated measure in healthy children and adults; (b) training was carried out a minimum of once per week for at least four weeks; (c) published in a peer-reviewed English language journal or on a pre-print server. Results: The main model for fat mass effects revealed a trivial standardized point estimate with high precision for the interval estimate, with moderate heterogeneity (−0.016 (95%CI −0.07 to 0.04); I2 = 36%). The main model for fat-free mass (FFM) effects revealed a trivial standardized point estimate with high precision for the interval estimate, with negligible heterogeneity (−0.0004 (95%CI −0.05 to 0.05); I2 = 16%). The GRADE summary of findings suggested high certainty for both main model effects. Conclusions: Our findings provide compelling evidence that the pattern of intensity of effort and volume during endurance exercise (i.e., IT vs MICT) has minimal influence on longitudinal changes in fat mass and FFM, which are likely to minimal anyway. Trial registration number: This study was preregistered on the Open Science Framework.