Pranic Agriculture (PA) is an emerging supplementary farming system applied to the seeds, soil, and seedlings to improve plant growth and yield by improving the quality and quantity of Prana using Pranic Healing techniques. Chilli is the major spice crop of India. There is a constant demand for chilli in the local and international markets; necessitating its increased production. A field study (0.2 h) was carried out to understand the influence of Pranic agriculture treatment on chilli plant growth parameters, flowering, yield traits and molecular changes at the DNA level by Random Amplified Polymorphic DNA (RAPD) marker analysis. Plant height was significantly (p < 0.05) higher in pranic treatment by 21% than in control. Leaf Chlorophyll content and root length were increased by 13% and 44% respectively in pranic treated chilli than control. Pranic treatment showed significantly higher fruit weight (6.47 g), the number of seeds per fruit (64.5), and yield per acre (14.25 t) as compared to control (5.56g, 51.1 and 12.21t) respectively. RAPD marker analysis recorded an average polymorphism of 24% between pranic and control. Pranic treatment was found effective in increasing the growth and yield of chilli. PA would be a supportive farming system for attaining sustainable and eco-friendly agriculture.