High efficiency in the analytical workflow, including fast sample preparation and LC-MS/MS analysis, is an advantage when analyzing a high number of samples. It can however be a challenge when determining polar analytes in complex, biological samples, and one must expect to make a compromise between a simple sample preparation followed by a long chromatographic separation, or vice versa, to limit matrix effects. In this proof-of-concept work, a one-step 96-well (parallel extraction) electromembrane extraction (EME) method was coupled to flow injection-MS/MS of 0.7 min per sample, allowing a very high-throughput analysis of 12 polar, endogenous metabolites from unprecipitated plasma of limited dilution. The throughput of the EME method matched the subsequent analysis. Recoveries ranged from 6 to 93 %, and repeatability and linearity were 2-15 % and R-2 >= 0.9949, respectively, for all but two compounds. Matrix effects were approximately 50 % after EME and varied <11 % between 6 plasma donors, which represented a major improvement relative to a simple protein precipitation where signals were entirely suppressed. The work demonstrates a potential for EME coupled to flow injection-MS/MS to serve as a high-throughput platform for bioanalysis, not just of polar analytes, but also hydrophobic drugs both basic and acidic.