Aims: Three pre-PCR processing strategies for the detection and/or quantification of Salmonella in naturally contaminated soya bean meal were evaluated. Methods and Results: Methods included: (i) flotation-qPCR [enumeration of intact Salmonella cells prior to quantitative PCR (qPCR)], (ii) MPN-PCR (modified most probable number method combined with qPCR) and (iii) qualitative culture enrichment PCR. The limit of quantification was 1·8 × 102 CFU g-1 (flotation-qPCR) and 0·02 MPN g-1 (MPN-PCR). Fifteen naturally contaminated Salmonella positive soya bean meal samples from one lot were analysed in parallel with the three methods, using 2·5, 50 and 25 g of feed, respectively, resulting in detection of Salmonella in 6, 15 and 9 bags. Enumeration resulted in 1·8 × 102-7·8 × 103 CFU g-1 (flotation-qPCR) and 0·024 to >5·2 MPN g-1 (MPN-PCR). Conclusions: Except for differences in methodology, results obtained with the three techniques could be due to the presence of nonculturable Salmonella and/or a heterogeneous distribution of Salmonella in the material. Significance and Impact of the Study: The evaluated methods provide different possibilities to assess the prevalence of Salmonella in feed, together with the numbers of culturable, as well as nonculturable cells, and can be applied to generate data to allow more accurate quantitative microbial risk assessment for Salmonella in the feed chain. © 2013 The Society for Applied Microbiology.