The method for isolating nucleic acids from a food sample comprising the following steps: a) obtaining a food enrichment culture; b) transferring a portion of the food enrichment culture into a reaction vessel thereby providing a food enrichment sample and providing a water-immiscible phase in contact with the food enrichment culture; c) lysing the food enrichment sample to provide a lysed sample; d) isolating nucleic acids from the lysed sample. Food enrichment culture samples are known to contain high concentrations of organic and/or liposoluble inhibitors. By contacting the enrichment culture sample with a water-immiscible phase before the actual DNA extraction procedure starts, part of the lipophilic inhibitors is expected to cross the phase interface due to an enhanced solubility in the organic phase and thereby become depleted. The water-immiscible phase provided according to the invention interacts directly with the sample material throughout bacteria lysis and DNA extraction thereby optimizing the subsequent DNA purification processes due to the depletion of food-borne inhibitors. This method yields nucleic acids, in particular DNA that is of an improved quality and purity to be used in a subsequent PCR reaction to detect pathogen nucleic acids in the isolated nucleic acids.