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Heart Rate Variability (HRV) and respiratory sinus arrhythmia are directly associated with autonomic flexibility, self-regulation and well-being, and inversely associated with physiological stress, psychological stress and pathology. Yoga enhances autonomic activity, mitigates stress and benefits stress-related clinical conditions, yet the relationship between autonomic activity and psychophysiological responses during yoga practices and stressful stimuli has not been widely explored. This experimental study explored the relationship between HRV, mood states and flow experiences in regular yoga practitioners (YP), non-yoga practitioners (NY) and people with metabolic syndrome (MetS), during Mental Arithmetic Stress Test (MAST) and various yoga practices. The study found that the MAST placed a cardio-autonomic burden in all participants with the YP group showing the greatest reactivity and the most rapid recovery, while the MetS group had significantly blunted recovery. The YP group also reported a heightened experience of flow and positive mood states compared to NY and MetS groups as well as having a higher vagal tone during all resting conditions. These results suggest yoga practitioners have a greater homeostatic capacity and autonomic, metabolic and physiological resilience. Further studies are now needed to determine if regular yoga practice may improve autonomic flexibility in non-yoga practitioners and metabolic syndrome patients. Clinical Trial No 'ACTRN 2614001075673'.