Diatomaceous earth (DE) is a sedimentary rock comprising fossilized shells of diatoms, which are a type of algae. The shells of the diatoms are made of silicon dioxide, which is also the main component of DE. DE has excellent moisture absorption and desorption properties and is widely used as an adsorbent, abrasive, insulator, catalyst, and carrier in the stationary phase. It has also been widely studied for its application as a new silicon material in emerging growth fields, such as biosensors. However, because organic matter is adsorbed on the surface of DE, the organic matter must be removed to exploit the properties of mesoporous silica. In this study, the organic matter on the DE surface was removed by alkali treatment to expose the pores and increase the adsorption capacity. Additionally, papain was physisorbed onto DE using a rotator, and l-cysteine was added for papain activation. Under these optimised conditions, the activation of the papain enzyme was effective, resulting in improved DE performance. The adsorption power of DE was correlated with the amount of papain adsorbed, which, in turn, was correlated with its absorbance. Trichloroacetic acid was added to stop the reaction, and the absorbance was measured. The prepared samples were designated as papain/DE (P/DE) complexes. The final concentration of the P/DE was 1 mg/mL. In addition, cross-linked and non-cross-linked P/DE samples were prepared using N-hydroxysuccinimide and water-soluble carbodiimide in a 5:3 ratio and compared. The results showed that surface treatment and functionalisation of DE improved its functionality (enzyme activity), indicating its potential as a new DE material.