In this work, an improved CE method for the medium-throughput determination of main organic acids (oxalate, malate, citrate), the amino acid glutamate and the sugars fructose, glucose and sucrose in several food matrices is described. These compounds have been identified as key components in the taste intensity of fruit and vegetable crops. Using a running buffer with 20 mM 2,6-pyridine dicarboxylic acid pH 12.1 and 0.1% hexadimethrine bromide, replacing it every 5 h to avoid pH decrease, and optimizing capillary conditioning between runs with 58 mM SDS during 2 min at 20 psi, it is possible to effectively quantify these compounds while increasing medium throughput repeatability. This procedure resolves problems such as increases in migration time and reduction of resolution between problematic peaks (malate/citrate and fructose/glucose) detected in a previous method. The new procedure even considerably reduced time analysis down to 12 min. Under optimal conditions, a large number of injections (200) could be administered without any disturbances in the same capillary. The reliability of the proposed method was further investigated with several food matrix samples, including tomato, pepper, muskmelon, winter squash, and orange. This method is recommended for routine analysis of large number of samples typical of production quality systems or plant breeding programs.