The aim of this review was to collect and systematize results of studies from the last 5 years concerning the influence of the Pilates method (PM) on functional body composition (FBC). Methods: The criteria of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) were used in this review. We conducted research in three scientific databases: (i) Web of Science Core Collection, (ii) SCOPUS, and (iii) search directory of the library catalog of the Faculty of Sport and Physical Education of the University of Coimbra—EBSCO Discovery Services. We found 334 articles, covering the period between 1 January 2017 and 31 December 2021. After the selection process, we found 33 eligible articles. Results: The main results seem to point to a tendency to get a better body weight and body fat percentage (BFP), hip circumference (HC), waist, and skinfolds from the chest, abdomen, triceps, and supra-iliac in mostly female samples. Available evidence indicates that, in body composition (BC) and FBC, Pilates practice tends to be effective in reducing obesity as a multifactorial condition. Conclusions: It is concluded that there is a marked trend in the benefits of Pilates in FBC, which is in line with other systematic reviews at the BC level (which includes body weight (BW) and body mass index (BMI)) and in the reduction of the percentage of fat mass (FM). It is also concluded that there is a vast lack of studies on the male population, preventing further scientific development in this area. The limitations of this systematic review can be overcome with studies that bring together multidisciplinary aspects of FBC, better designed and methodologically more robust, which will allow more reliable analyses for the implementation of the Pilates method in terms of FBC. In addition, further studies with a male sample or mixed samples (men vs. women) could confirm the trend of no gender differences in the benefits of Pilates practice.