PURPOSE: Hypertension is associated with autonomic nervous system (ANS) dysregulation. Heart rate variability (HRV) monitoring is frequently used as a gauge of the ANS balance. The aim of the present study was to assess the effects of yoga and naturopathy on the autonomic variables in patients with hypertension. METHODS: 262 hypertensive patients were randomly allocated to the study group (SG) or control group (CG) in a randomized controlled trial. For ten days, the SG (n = 131) group got received naturopathic treatments and yoga, whereas the CG (n = 131) group did not. HRV which was examined at the beginning and end of the 10-day intervention period and again after 9 months, served as the study's main endpoint. RESULT: There was a significant change in the frequency domain of heart rate variability with a significant increase in High frequency (HF) and a significant decrease in low frequency (LF) and LF/HF (all p < 0.05) were observed after follow-up in both SG and CG, but the magnitude of change was more in SG with a significant difference in LF/HF between group. CONCLUSION: Results of this study suggest that 10 days of integrated yoga and naturopathy intervention produces a shift of vagal activity towards parasympathetic activity. CLINICAL TRIAL REGISTRATION NUMBER: CTRI/2019/01/016883.