A number of studies have focused on the selection and use of new biocontrol agents, but the effects of the introduction of these microorganisms on non-target organisms, including the crop plants themselves, are not well known. Non-target effects of sprayed applications of a potential biocontrol agent of apple powdery mildew (Podosphaera leucotricha Ell. Et Ev.), on scab infections (Venturia inaequalis Cooke Winter), on codling moth [Cydia pomonella L. (Lepidoptera: Tortricidae)] oviposition and damage and apple (Malus x domestica) fruit quality are examined. This biocontrol agent, an epiphytic yeast isolate called Y16, affected neither conidia germination of V. inaequalis nor their penetration of the leaf tissue but suppressed the disease caused by this pathogen. The quantity of eggs laid by the codling moth during its second flight period on yeast treated trees was significantly different to the quantity of eggs laid on the untreated trees. In the first season of the experiments, more eggs were laid on the treated trees, especially on those tree parts closest to the fruit. These results, however, were not confirmed the following season: fewer eggs were laid on the treated trees than on the untreated trees. These conflicting observations are attributed to year-to-year variation in environmental conditions, which may affect yeast survival and activity. A 2-month-long assay was conducted in the orchard during the codling moth's second flight period from mid-July until mid-September. The yeast treatment did not affect the damage caused by the codling moth to the fruits. Finally, the yeast treatment did not affect any of the examined fruit quality parameters.