This study aimed to investigate the effect of commercial non-Saccharomyces yeasts and Oenococcus oeni on the formation of amino acid derivatives, some of which have neuroactive properties, during fermentation in laboratory-scale processing of white and red wines. Changes in the content of amino acid derivatives during fermentation of large-scale white and red wines were also evaluated. The highest kynurenic, picolinic, and quinolinic acid concentrations were observed in white wine fermented with Torulaspora delbrueckii, Kluyveromyces thermotolerans and Saccharomyces cerevisiae simultaneously. No changes in the content of picolinic and kynurenic acid were observed during large-scale white wine fermentation. Tryptophan ethyl ester concentration in all wines increased significantly during alcoholic fermentation. Natural and O. oeni malolactic fermentation did not alter the content of picolinic acid, a neuroprotective compound, in red wine. The decrease in the content of tyramine, phenylethylamine, and dopamine in laboratory-scale white wines was observed during alcoholic fermentation.