For the isolation of the ingredients required for functional foods and nutraceuticals generally membrane filtration has too low a selectivity and chromatography is (too) expensive. Electro-membrane filtration (EMF) seems to be a breakthrough technology for the isolation of charged nutraceutical ingredients from natural sources. EMF combines the separation mechanisms of membrane filtration and electrophoresis. In this study, positively charged peptides with antimicrobial activity were isolated from an alpha(s2)-casein hydrolysate using batch-wise EMF. alpha(s2)-Casein f(183-207), a peptide with strong antimicrobial activity, predominated in the isolated product and was enriched from 7.5% of the total protein components in the feed to 25% in the permeate product. With conventional membrane diafiltration using the same membrane (GR60PP), isolation of this and other charged bioactive peptides could not be achieved. The economics of EMF are mainly governed by the energy costs and the capital investment, which is affected by the flux of the desired peptide. A maximum average transport rate of alpha(s2)-casein f(183-207) during batch-wise EMF of 1.2 g/m2. h was achieved. Results indicate that an increase in the hydrolysate (feed) concentration, the applied potential difference and the conductivity of the permeate and electrode solutions, and a reduction in the conductivity of the feed result in a higher transport rate of alpha(s2)-casein f(183-207). This is in line with the expectation that the transport rate is improved when the concentration, the electrical field strength, or the electrophoretic mobility is increased, provided that the electrophoretic transport predominates. The expected energy consumption of the EMF process per gram of peptide transported was reduced by approximately 50% by applying a low overall potential difference and by processing desalinated hydrolysate. Considerable improvements in transport rate, energy efficiency, and process economics seem to be attainable by additional optimization of the process parameters and the EMF module design.