Fungal pathogens such as Botrytis cinerea, Penicillium expansum and the Gloeosporioides group are mainly responsible for important economical losses of post-harvest apples. Application of biological control agents (BCAs) is an emerging alternative to synthetic fungicides. However, before becoming an economically feasible alternative to chemical control, BCAs have to satisfy different requirements related to biological, technological and toxicological properties. The different steps for a successful strategy of disease control (selection, production and formulation, study of mechanisms of action, ecological characterization, molecular monitoring, pilot efficacy trials, registration) are reviewed in this paper considering the antagonistic yeast Pichia anomala strain K. This strain was selected for its high and reliable antagonistic activity against B. cinerea and P. expansum on apples. The studies of mode of action and ecological fitness are emphasized because they can lead to a better efficacy of strain K. Recently advanced molecular techniques have contributed to improving knowledge on the modes of action. Thanks to the identification of genes involved in biocontrol properties, the genetic basis of action mechanisms can be understood. That approach was adopted for P. anomala strain K and led to the identification of genes coding for exo-β-1,3-glucanases implicated in the efficacy. Based on that identification, a formulation involving β-1,3-glucans was developed and applied with higher efficacy in controlled conditions. The importance of ecological characterisation is also highlighted in the context of pre-harvest application of P. anomala strain K. UV light, temperature and humidity were identified as major factors influencing the strain K population. A model taking into consideration temperature and humidity was developed and could be useful in deciding whether pre-harvest treatment is sufficient to allow fast colonization of wounds prior to the arrival of wound pathogens, or whether it is wise to apply further post-harvest treatment to increase the yeast population density. This summary presenting 20 years of work also paid attention to practical application of strain K and its integration with other methods of control.