Flower emasculation is commonly used to make flowers unattractive to pollinating insects and to carry out controlled pollinations. In sweet cherry, we have observed recurrent low fruit set after flower emasculation and compatible pollination without apparent causes. This led us to evaluate its effect on the progress of the reproductive phase and on fruit set in this species. Flower emasculation reduced by more than a half the fruit set obtained in crosses made during two consecutive years. This effect could be traced back to the first week after anthesis where weight increase of pistils from emasculated flowers was smaller and ovule degeneration was accelerated compared to pistils from non-emasculated flowers. Pollen tubes, which behaved similarly at the stigma-style level in emasculated and non-emasculated flowers, lost their directionality in the area close to the degenerated ovule in the ovary. While flower emasculation is valid to evaluate pollen tube performance in the style and to determine incompatibility relationships, the lower fruit set registered after emasculation alerts on its use in fruit set experiments and breeding programs.