“Vrikshayurveda”, an ancient literature collection of plant life science depicted importance of kunapajala, a fermented liquid organic manure sourced from animal origin. It is an excellent organic fertilizer influencing a wide range of crops with enhanced growth and development. During later days, “kunapajala” with vegetarian ingredients, without nutrient compromise was developed and standardized. It includes ingredients viz., soybean meal, paneer, tofu, rice husk, black gram, groundnut oilcake, cow dung, urine, honey, ghee and milk. The fermented formulation has essential nutrients, amino acids, keratins etc. which applied on plants, naturally flourished with excellent growth, flowering and fruiting. In this study, the fermented liquid organic manure kunapajala at 20th, 40th and 60th day of fermentation period was analysed for its bioactive compounds using the analytical technique Gas Chromatography – Mass Spectrometry (GC-MS). Extract was prepared using organic solvents diethyl ether and methanol. The mass spectra of compounds matched with Wiley's standard mass spectrum database and National Institute of Standards and Technology's (NIST) libraries. This study unfolded the presence of various compounds like Hexanoic acid, Phenol-TMS, Methyl oleate, Octadecanoic acid, Methyl palmitate, Myristic acid-TMS, Tetradecanoic acid, Caproic acid, Methyl myristoleate; (Z)-tetradec-9-enoic acid, 2-Aminooctanoic acid-TMS; 2-aminooctanoic acid, Butylated Hydroxytoluene, Juniperic acid-2TMS, Stearic acid-TMS, Linoleic acid-TMS etc. These phytochemicals have antimicrobial, antifungal, antibacterial, physiological and metabolic responses, antioxidant, Insecticidal irritant and nematicidal activities which effectively influence organic crop production. The result indicated the vital role of kunapajala as an effective source of liquid formulation through its phytochemical importance.