Grey mould caused by Botrytis cinerea presents significant challenges to apple production including organic farming. Biocontrol yeasts and their consortia can limit fungal diseases. This study evaluates the efficacy of selected yeast isolates and their consortia in suppressing B. cinerea in stored apples. The yeast strains tested—Wickerhamomyces anomalus 114/73, Naganishia albidosimilis 117/10, and Sporobolomyces roseus 117/67—were assessed at 4 °C and 23 °C, individually and in consortia. The results demonstrate the superior efficacy of a consortium combining all three isolates, which achieved the highest reduction in spore germination and disease severity. A two-strain consortium of isolates 114/73 and 117/10 also showed substantial biocontrol activity, outperforming single-strain treatments. These combinations effectively suppressed B. cinerea growth and displayed rapid colonization of apple wounds. The study highlights the potential of yeast isolates and their consortia to manage postharvest fungal decay, addressing a critical need for sustainable, eco-friendly solutions in organic apple production.