Crude red palm oil of 8.7% free fatty acid content was deacidified using enzyme (lipase from Rhizomucor miehei), solvent (ethanol) and chemical (aqueous Sodium hydroxide) and its impact on chemical characteristics and composition were evaluated. Deacidification of oil using enzyme showed nearly 100% product yield. The neutral lipid loss after ethanol and sodium hydroxide deacidification of the oil was 13.6% and 19.5% respectively. The enzyme deacidified oil has shown a higher value in unsaponifiable matter (0.91%), monoacylglycerols (2.8%) and diacylglycerols (18.7%) contents as compared to the other two methods of deacidification. Also it showed a higher retention of nutraceuticals such as carotenoids (94%), phytosterols (57%), total tocopherols (71%), squalene (72%), coenzyme Q₁₀ (99%) and total phenolics (69%) with IC₅₀ value of 19.7 mg of oil/ml. Stearin content increased in the oil after deacidification with enzyme (47.4%) compared to the stearin content of crude red palm oil (28.6%). The olein fraction contained less saturated fatty acids (41.6%) than the fraction obtained by other two methods (47.2%). The enzyme catalyzed the esterification reaction of free fatty acids in crude red palm oil with added glycerol at 63°C with a rotation speed of 150 rpm under vacuum of 5 mmHg for the period of 12 h showed that enzyme based deacidification can be effectively utilized for the preparation of low acidic nutraceutical retained red palm oil.