A fruit snack with probiotics that is stable at room temperature is manufactured by combining various ingredients including fruit juices/purees to produce a slurry and cooking the slurry to produce a center that contains a high moisture content. The fruit snack center is covered with a barrier layer which in turn is covered by an outer layer that contains heat sensitive ingredients, such as probiotic cultures. The barrier layer substantially prevents migration of moisture from the center to the outer layer, and the fruit snack is cooled prior to applying the outer layer to minimize damage/harm to the heat sensitive ingredients. In addition to including probiotic cultures and being stable at room temperature, the fruit snack has other desirable characteristics including a chewy soft texture and fruit-flavorings, and may be manufactured using traditional processes.