Fouling during membrane emulsification due to biomolecule adsorption is still a drawback for broader applicability and a better holistic understanding is needed. This study aimed to investigate the fouling effect on the membrane and the enzyme being modified due to adsorption. Therefore, a lipase solution with varying concentrations and pH was filtered through a silica-based membrane. The degree of adsorption, membrane properties (microstructure and phase wetting), and enzymatic characteristics (conformation and activity) were evaluated. For insights on the molecular level, molecular dynamic simulations of the conformational changes of lipase caused by adsorption were performed. Regarding the membrane, an increase in lipase concentration increased the adsorption leading to higher fouling and decreased wetting implying a higher hydrophobicity of the membrane. Additionally, SEM showed that the pH of the lipase solution modified the microstructure of the foulant layer. Regarding the impact on the lipase, molecular dynamic simulations revealed an increase in the hydrophobic surface area, a rearrangement of the C-alpha atoms of the protein backbone, and an increase in the radius of gyration. Despite leading to enzyme mass loss, both the secondary structure and the activity showed no significant differences after processing, which might be due to the reversible adsorption.