Among the different anthropogenic stimuli humans are exposed to, the psychological and cardiovascular effects of auditory stimuli are less understood. This study aims to explore the possible range of change after a single session of auditory stimulation with three different ‘Modes’ of musical stimuli (MS) on anxiety, biomarkers of stress, and cardiovascular parameters among healthy young individuals. In this randomized control trial, 140 healthy young adults, aged 18–30 years, were randomly assigned to three MS groups (Mode/Raga Miyan ki Todi, Malkauns, and Puriya) and one control group (natural sounds). The outcome measurements of the State-Trait Anxiety Inventory, salivary alpha-amylase (sAA), salivary cortisol (sCort), blood pressure, and heart rate variability (HRV) were collected at three time points: before (M1), during (M2), and after the intervention (M3). State anxiety was reduced significantly with raga Puriya (p = 0.018), followed by raga Malkauns and raga Miyan Ki Todi. All the groups showed a significant reduction in sAA. Raga Miyan ki Todi and Puriya caused an arousal effect (as evidenced by HRV) during the intervention and significant relaxation after the intervention (both p < 0.005). Raga Malkauns and the control group had a sustained rise in parasympathetic activity over 30 min. Future studies should try to use other modes and features to develop a better scientific foundation for the use of Indian music in medicine.