The present invention relates to the bioupgrading of crude oil is directed to a process for decreasing the acidity of an acidic crude oil, comprising contacting an acidic crude oil with a mixture nitrogen containing compounds selected from the group comprising ammonia, ammonia hydroxide, amines and the salts thereof, and in the presence of lipase enzyme, under conditions of suitable temperature and pressure sufficient to form the corresponding amide. The resulting naphthenic acid derived amides can then be processed normally in a refinery using such processes as cracking or hydrotreating and converted to hydrocarbon, ammonia and carbon dioxide without causing damage to the refinery infrastructure. This enzyme process is done at reduced temperatures (40-60° C.) and pressures requiring less energy.