Procyanidins are phenolic oligomers, mainly composed of (+)-catechin and (-)-epicatechin units that exhibit certain sensorial and physiological properties of interest (e.g., astringency and bitterness of food, antioxidant activity, etc.). This paper shows the development of a micellar electrokinetic chromatography (MEKC) method for the separation of three procyanidin dimers (B1, B2, and B3), their monomers ((+)-catechin and (-)-epicatechin), and the cis- and trans-forms of p-coumaric acid. Separation conditions are optimized in terms of buffer pH, SDS concentration, and washing routine between injections. The best results in terms of peak resolution and reproducibility between separations were obtained with a MEKC running buffer at pH 5 with 100 mM SDS and a washing routine that includes a rinse step with 0.1 M sodium hydroxide. Using this new MEKC method it is possible to separate in less than 5 min the seven substances. More interestingly, it is demonstrated that the low pH used in this MEKC method allows one to obtain clean electropherograms when samples are injected. The method is shown to be reproducible between different days with relative standard deviation (RSD) values lower than 1% for migration times and lower than 7% for peak areas (3 days, 24 injections). The usefulness of this procedure to determine these compounds in effluents from food processing (i.e., soaking water from lentils, white beans and black beans) and in food by-products (i.e., almond peels) considered as potential procyanidin sources is demonstrated. To our knowledge, this is the first report of separation and determination of procyanidins in food samples done by capillary electrophoresis.