Biotechnological processes for the partial degradation or transformation of poly(cis-1,4-isoprene) rubber have been investigated during recent decades with promising results. The use of the enzyme ‘latex clearing protein’ (Lcp) to transform the polymer into more hydrophilic oligo-isoprenoids results in modifications of the rubber structure and the synthesis of new material. In order to find an alternative process to recover the degradation products, a continuous extraction method using a biphasic system is described. The enzymatic activity of Lcp1VH2 was studied in the presence of ethyl acetate and pentane as extraction solvents. Oligo(cis-1,4-isoprene) molecular species were isolated from the organic phase and analyzed by Electrospray Ionization Mass Spectrometry. The enzymatic reaction process was evaluated in terms of the biotransformation yield of poly(cis-1,4-isoprene) rubber into the corresponding degradation products. Biotransformation yields of between 42–52 % were achieved depending on the enzymatic reactor design and the extraction solvent. The results also showed that the mass distribution of the oligo(cis-1,4-isoprene) depended on the organic solvent applied. A novel, simple and effective process is demonstrated for biotransformation of poly(cis-1,4-isoprene) rubber with high oligo-isoprenoid molecules recovery yields.