Our country boasts an extensive collection of stone monuments. Employing traditional techniques for rubbings on these artifacts allows for the limitless replication of their inscribed content, serving both dissemination and preservation purposes. However, improper handling during the rubbing process can lead to ink contamination on the surface of these relics. A prevalent issue is that a significant number of stone monuments in China are dense ink layers that obscure their original appearance, rendering it challenging to discern the pre-existing characters and patterns on stone surfaces. The main approach to the removal of ink contamination on the surfaces of stone monuments is conventional physical cleaning methods. These methods lack the requisite specificity to selectively target the inky residues. Comprising solid carbon black particulates mixed with animal glue and water, the ink is subjected to pounding repeatedly before becoming dry. Subsequently, the ink adhered to the stone surface using animal glue as an adhesive forms indelible traces that are difficult to remove. This animal glue is predominantly constituted by proteins. By disrupting the protein within the animal glue, its adhesive properties are lost, and thus the ink will lose its ability to adhere to the stone surface. To verify this concept, our study compared the property of protein enzymes to hydrolyze the main protein component of animal glue, investigating the efficacy of bio-cleaning agents formulated from different protein enzymes and comparing them with conventional physical cleaning methods. The effectiveness of various cleaning materials was assessed through comparative analyses of photographs, microscopic images and chromatism before and after cleaning. Experimental results demonstrate that enzyme cleaning agents formulated with surfactants exhibited more noticeable ink removal effects compared to deionized water and ethanol. Among enzyme materials, a 1% alkaline protease solution achieved the best ink removal results. Formulating enzyme materials with sodium dodecyl sulfate (SDS) and aliphatic alcohol polyethylene ether (AEO₉), experiments indicate that the best cleaning performance was achieved when alkaline protease was combined with AEO₉. Incorporating liquid cleaning agents on vertically oriented stone monuments leads to fluidity issues and contaminates the experimental area. To enhance adhesion, gel materials were employed. Various gel materials were tested, and the gel produced using enzyme agents in conjunction with Carbopol 940 exhibited the best adhesion performance on stone monuments. This improves contact between the cleaning material and the artifact surface, significantly enhancing cleaning efficacy. This gel-based approach is suitable for carrying cleaning agents applied to stone monuments. Two on-site experiments were conducted on the surface of inscriptions within the “Inkstone Studio Reviews” collection at Xi’an Beilin Museum. Deionized water, ethanol, liquid enzyme materials, surfactants and cleaning gels were employed for these experiments. The experiments reveal that the cleaning gel produced using AEO₉ and Carbopol 940 exhibited superior cleaning effectiveness compared to other liquid cleaning materials. Moreover, this gel could even effectively clean ink traces in crevices on the surface of stone monuments without affecting the artifacts themselves.