Due to the need for environmental protection and sustainability, there has been a rising need to replace the traditionally harsh oxidative functionalization process, which is essential for syntheses of various organic compounds, by biocatalysis. However, the investigated alternative processes are still challenged with enzyme instability and/or low specific reaction rate. Due to these still existing challenges and the recognition of Pickering emulsions as an efficient platform for continuous biphasic biocatalysis, the first, enzymatic step of the lipase catalyzed oxidative functionalization was investigated in bioactive Pickering emulsions. The study focused on the impact of Pickering emulsion composition such as the volume phase fraction, type and concentration of the nanoparticles and enzymes on continuous peroxyacetic acids synthesis. The type of nanoparticles used and Candida antarctica lipase B concentration significantly impacted the process while the other named parameters only had a marginal influence.