The technical application of biocatalysts is commonly realized in aqueous media limiting the range of reactants to hydrophilic compounds. The use of Pickering emulsions (PEs), where biocatalysts are immobilized in water droplets stabilized by nanoparticles and surrounded by solvent containing the substrates, presents an alternative for reactions involving hydrophobic reactants. While batch PE biocatalysis has been demonstrated for a variety of reactions and enzymes, no continuous process at industrially relevant residence times has been reported yet. Here, a continuous membrane reactor is proposed to retain the aqueous drops containing the enzymes in the reactor while the product containing permeate is continuously filtered through the membrane. To identify main influencing factors on membrane operation, the impact of enzyme properties and concentration of nanoparticles on drop size distribution (DSD) and filterability was investigated. It was found that enzyme properties have a strong impact on both DSD and filtration. With lipases, PEs showed an improved filterability and reproducibility. Higher particle concentrations lowered the flux through the membrane due to unbound particles forming the filter cake. Thus, particle concentration should be kept as low as possible. The concept was proven by a continuous lipase catalyzed transesterification with the enzyme remaining active in the PE.