Arginine, an abundant amino acid in kimchi, is metabolized by lactic acid bacteria (LAB) with arginine deiminase (ADI) genes, producing ammonia and thereby increasing nitrate and nitrite levels. Therefore, fermentation strategies aimed at reducing arginine catabolism are needed. Unlike other LAB, Leuconostoc mesenteroides lacks ADI genes. To examine the impact of fermenting kimchi with an L. mesenteroides starter culture, we compared naturally fermented kimchi (kimchi A) and starter-fermented kimchi (kimchi B). In kimchi A, diverse LAB species were detected, whereas kimchi B mainly included L. mesenteroides. LC-MS/MS and multivariate analyses identified key metabolic differences. Orthogonal partial least squares-discriminant analysis (OPLS-DA) revealed a clear separation between kimchi A and B. Notably, malic acid, citric acid, and arginine showed significant differences, with high variable importance in projection (VIP) scores; these are essential in malolactic acid fermentation. Correlation analyses demonstrated strong links between L. mesenteroides and these metabolic changes. L. mesenteroides lacks genes for malic and citric acid catabolism, confirming its role in preventing malolactic acid fermentation and nitrogen cycling and supporting its value for enhancing kimchi safety and taste.