Nowadays, there are many sorts of beer, however, some of them, despite the good sensory and other quality indicators, could contain high concentrations of undesirable compounds, such biogenic amines (BA). The yeast strain (YS), used for fermentation, can cause desirable as well as undesirable changes in beer. The aim of this study was to evaluate the contribution of different YS (A-Saccharomyces cerevisiae var. diastaticus, B-Saccharomyces cerevisiae var. bayanus, C-Brettanomyces claussenii) on the main quality parameters of beer. In addition, the BA concentration and the volatile compounds (VC, measured by gas chromatography–mass spectrometry) and their relation with beer overall acceptability (OA, evaluated by 20 trained judges) and emotions induced for consumers were analysed. The YS was a significant factor on alcohol formation in beer (p = 0.0001). The highest colour intensity was shown by C beer (10.2 EBC), and the latter beer showed the lowest OA. All of the beer samples induced the highest intensity of the emotion “neutral”, and the main VC of the beer were 3-methyl-1-butanol; L-α-terpineol; hexanoic acid 3-methylbutyl ester; and n-capric acid isobutyl ester. The highest total BAs content was found in beer fermented with C. Finally, all of the tested YS are suitable for beer production, however, taking into consideration the safety aspect of the beer, it should be mentioned that the highest concentration of BAs was found in beer fermented with C strain.