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Three <i>Metschnikowia</i> strains marketed as bioprotection yeasts were studied to compare their antimicrobial effect on a mixture of two <i>Hanseniaspora</i> yeast strains in synthetic must at 12 °C, mimicking pre-fermentative maceration by combining different approaches. The growth of the different strains was monitored, their nitrogen and oxygen requirements were characterised, and their metabolomic footprint in single and co-cultures studied. Only the <i>M. fructicola</i> strain and one <i>M. pulcherrima</i> strains colonised the must and induced the rapid decline of <i>Hanseniaspora</i>. The efficiency of these two strains followed different inhibition kinetics. Furthermore, the initial ratio between <i>Metschnikowia</i> and <i>Hanseniaspora</i> was an important factor to ensure optimal bioprotection. Nutrient consumption kinetics showed that apiculate yeasts competed with <i>Metschnikowia</i> strains for nutrient accessibility. However, this competition did not explain the observed bioprotective effect, because of the considerable nitrogen content remaining on the single and co-cultures. The antagonistic effect of <i>Metschnikowia</i> on <i>Hanseniaspora</i> probably implied another form of amensalism. For the first time, metabolomic analyses of the interaction in a bioprotection context were performed after the pre-fermentative maceration step. A specific footprint of the interaction was observed, showing the strong impact of the interaction on the metabolic modulation of the yeasts, especially on the nitrogen and vitamin pathways.