This study starts from the need to remove a mix of proteins, oils and natural resin, called beverone in the Italian literature, from the back of canvas paintings. The aim of this study is to develop and evaluate the effectiveness of two different agarose/enzyme gels containing, respectively, a trypsin derived from porcine pancreas and a lipase from Candida rugosa, both in an aqueous solution of deoxycholic acid-triethanolamine soap. Enzymes were selected because of their action on peptide and ester bonds, effectiveness at maintaining a weak alkaline pH and low cost. Several series of model samples, resulting from a combination of rabbit skin glue, linseed oil and colophony, were prepared to test the enzyme gels with two different values for each of the following variables: agarose concentration, application modes and time of application. Measurements of weight loss after the gel application and Fourier transform infrared analysis were conducted to underline the hydrolysis occurring due to the enzyme gels and their effectiveness. Results confirmed what has been found in the literature and improved our knowledge about the action of agarose enzyme gels on complex substrates (hydrophilic/hydrophobic). The gels applied fluidly, with a longer contact time and a lower agarose concentration, are more effective. Furthermore, trypsin gels provided better results on substrates with oil and glue, while lipase gels turned out to be more effective on substrates made of a mix of oil, glue and colophony.