Electromembrane extraction (EME) was performed on samples containing substantial amounts of NaCl to investigate how the presence of salts affected the recovery, repeatability, and membrane current in the extraction system. A group of 17 non-polar basic drugs with various physical chemical properties were used as model analytes. When EME was performed in a hollow fiber setup with a supported liquid membrane (SLM) comprised of 2-nitrophenyl octyl ether (NPOE), a substantial reduction in recovery was seen for eight of the substances when 2.5% (w/v) NaCl was present. No correlation between this loss and the physical chemical properties of these substances was seen. The recovery loss was hypothesized to be caused by ion pairing in the SLM, and a mathematical model for the extraction recovery in the presence of salts was made according to the experimental observations. Some variations to the EME system reduced this recovery loss, such as changing the SLM solvent from NPOE to 6-undecanone, or by using a different EME setup with more favorable volume ratios. This was in line with the ion pairing hypothesis and the mathematical model. This thorough investigation of how salts affect EME improves the theoretical understanding of the extraction process, and can contribute to the future development and optimization of the technique.