The aim of the present study was to investigate the impact of two lager brewing yeasts (KVL001 and KVL018), known to produce different levels of sulfite and thioredoxin, on the flavor stability of beer during storage for 24 weeks at 25 °C and 35 °C. Fermentations with the two yeast strains were carried out in two identical pilot scale brews and provided fresh beers with very similar sensory profiles, only differing significantly in content of sulfite, iron, thioredoxin, and free amino acids. No difference in protein thiols was observed indicating that thioredoxin was not active in the final beer. The yeast strain KVL018 consumed less free amino acids than KVL001 resulting in fresh beers with a higher content of free amino acids. During storage, the beers developed very similarly, but the beers fermented with KVL018 developed more 'fruity aged/vinous' flavor, especially at 35 °C. This suggested that a higher degree of the Maillard reaction took place in these beers due to the higher content of free amino acids. Beers fermented with KVL018 also contained more sulfite and less iron, but scored lower in the general evaluation of the sensory analysis. In conclusion, our results indicate that the yeast strain (KVL001) taking up more free amino acids resulted in more flavor-stable beer due to a lower degree of the Maillard reaction, while no clear effects were observed on oxidation.