Background: Metabolic syndrome (MetS) influences the autonomic modulation, increasing the risk of cardiovascular events, which demands the identification of effective treatments for this population. Considering this, the study has the objective of evaluating the effects of periodized aerobic interval training (AIT) on geometrical methods of heart rate variability (HRV) on individuals with MetS. Methods: 52 individuals with MetS were considered for analysis. They were divided into two groups: aerobic interval training group (AITG; n = 26) and control group (CG; n = 26). The AITG performed 16 weeks of periodized AIT. For HRV analysis, the heart rate was recorded beat-by-beat at the beginning and the end of the AIT program and geometrical methods were used for analysis. Results: significant increase was observed for triangular index (RRtri, −1.25 ± 0.58 vs. 1.41 ± 0.57), standard deviation of distances from diagonal to points (SD1, −0.13 ± 1.52 vs. 4.34 ± 1.49), and standard deviation of distances from points to lines (SD2, −2.14 ± 3.59 vs. 11.23 ± 3.52) on AITG compared to CG. Significant differences were not observed for triangular interpolation of normal heartbeats interval histogram (TINN, −4.05 ± 17.38 vs. 25.52 ± 17.03) and SD1/SD2 ratio (0.03 ± 0.02 vs. 0.00 ± 0.02). Qualitative analysis of the Poincaré plot identified increase on dispersion of both short and long-term intervals between successive heartbeats (RR interval) on AITG after the AIT program. Conclusion: geometric indices of HRV suggest an increase in cardiac autonomic modulation in individuals with MetS after 16 weeks of periodized AIT.