The potential of the CE-based enzymatic assay has been demonstrated in case of a typical plant membrane enzyme - chlorophyllase. An efficient, automated and rapid semi-quantitative method has been developed, which allowed us to assess the activity of the enzyme via two strategies. Firstly, a reaction conducted in a vial placed directly on the sample tray was combined with the concomitant separation and detection of reagents. The method was used to monitor the reaction progress. Secondly, an online approach was applied using an electrophoretically mediated mixing. The reaction was performed in-capillary, resulting in an extreme reduction of the reagent amounts required for a single run. Both methods were effective in the assessment of the activity of a membrane enzyme, a member of protein class known to pose experimental difficulties.