Abstract: The invention relates to a method for extracting nucleic acids of microorganisms contained in a complex mixture, particularly a food mixture, comprising at least the following steps: the mixture is clarified; the microorganisms are retained on a filtering cartridge; said microorganisms are lysed; the nucleic acids are recovered, concentrated, and purified. The invention also relates to a filtering cartridge and an apparatus used for carrying out the inventive extraction method. Also disclosed is a device for extracting, detecting, and if necessary quantifying the nucleic acids of microorganisms contained in a complex mixture.