Despite the various standard non-linear measurements used in autonomic modulation (AM) assessments usually being applied to long time-series, such analyses can sometimes be applied to shorter term series. To overcome this disadvantage, chaotic global methods were formulated by putting together heart rate variability (HRV) linear methods. Chaos provides information about vegetative function control related to cardiovascular risks. Applying this method can be useful to investigate the complexity of the health condition after resistance training protocols, as a therapeutic intervention in AM in metabolic syndrome individuals (MetS). This study aimed to compare the effects of two resistance training programs (conventional vs functional) in MetS using nonlinear analysis of AM. MetS subjects (n=50) of both sexes aged 40 to 60 years were randomly divided into two programs; a group of 12 people served as a control group. Both groups performed 30 sessions of training. AM was assessed in the chaos domain by chaotic global techniques. The main results showed that both resistance training, functional and conventional, increased chaos when compared to the control group, respectively, observed by chaotic forward parameter (CFP)1 (13.9±17.9 vs 12.8±14.4 vs -2.23±7.96; P≤0.05) and CFP3 (15.4±19.8 vs 21.9±13.2 vs -4.82±11.4; P≤0.05). In addition, 30 sessions of both resistance programs increased chaos, and non-linear analysis enabled discrimination of AM after interventions when compared to the control group.