This paper presents a rational strategy to identify and quantify the components of a commercial extract of the lipase B of Candida antarctica that can be extended to the analytical investigation of other crude extracts of enzymes. These information provided the fundamental knowledge for the development of a methodology to obtain highly pure and catalytically active CALB enzyme. The commercial extract Lipozyme(®) was subjected to a series of analytical techniques that allowed determining the presence of a non-soluble fraction; nucleic acids; benzoate and sorbate species and a mixture of three proteins. Particularly, it is worth noticing that the Bradford assay using CALB as standard instead of BSA proved to be a more reliable and accurate methodology to quantify the protein content of the assayed enzymatic samples. Size exclusion chromatography coupled with anionic exchange chromatography using a non-conventional, easy to remove buffer system such as ammonia-ammonium acetate afforded a sample that retains 47% of the proteins (being CALB the only enzymatic component of the purified sample) with a hydrolytic activity higher than the crude extract.