A novel method using fluorescence-marked gene probes is introduced into beer analysis in the context of official food control. Two commercial test kits for the detection of Lactobacilli/Pediococci and Megasphaera/Pectinatus beer spoilage bacteria were used and compared to classical plating techniques. The new method was found to be very sensitive and convenient for the identification and assessment of hygienic risks in beer samples from all stages of production. Besides that, Fourier transform infrared spectroscopy (FTIR) in combination with multivariate data analysis was evaluated to detect beer spoilage directly from the sample without prior inoculation. However, the correlations of the FTIR calibrations showed only low sensitivity so that this approach is not yet usable in food control.