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The automated TEMPO system (bioMerieux) is based on the most probable number (MPN) method for the enumeration of micro-organisms in foods. In this study, we evaluated the performance of the TEMPO system as a diagnostic tool in comparison with the standard method in processed soy products.A verification study was conducted using artificially contaminated soy product samples such as soy protein isolate, water-soluble soy polysaccharides, soy milk and processed soy food. Five types of micro-organisms were analysed using the automated MPN method (total aerobic bacteria, total coliforms, Enterobacteriaceae, yeast and mould and Staphylococcus aureus) vs the standard plate method. The results from each of the methods were highly correlated (r > 0·95). Naturally contaminated processed soy products on the market were also studied. There were no discrepancies observed between the respective methods.TEMPO methods were equivalent to the corresponding standard plate methods with very good rates of agreement.The automated MPN method is more practical and reliable for in-house microbiological testing in processed soy products.