The changes in the nonanthocyanin phenolic composition during red wine malolactic fermentation carried out spontaneously and by four different starter cultures of the species Oenococcus oeni and Lactobacillus plantarum were examined to determine whether differences in nonanthocyanin polyphenolic compounds could be attributed to the lactic acid bacteria (LAB) strain that performs this important step of the wine-making process. The polyphenolic compounds were analyzed by high-performance liquid chromatography with photodiode array detection and HPLC with electrospray ionization-mass spectrometry detection. The malolactic cultures selected for this study were indigenous wine LAB strains from the A.O.C. Rioja (Spain). Results showed different malolactic behaviors in relation to wine phenolic compositions for O. oeni and L. plantarum, and also, a diversity was found within each group. The hydroxycinnamic acids and their derivatives, the flavonols and their glycosides, the flavanol monomers and oligomers, and trans-resveratrol and its glucoside were the main compounds modified by the different LAB. The wild LAB population exerted a greater impact in the wine content of some of these phenolic compounds than the inoculated selected monocultures of this study.