Euglena gracilis, a single-celled microalga with various trophic growth styles under different cultivation conditions, contains nutrients, such as ß-1,3-glucans, essential amino acids, fatty acids, vitamins, and minerals. It has recently attracted attention as a new health food. Among them, ß-1,3-glucans, paramylon of Euglena, is an insoluble dietary fiber and is well known as an immune booster, attenuator of obesity and diabetes, reducer of acute liver injury, and suppressor of atopic dermatitis, and other chronic inflammatory disorders. Recently, evidence has appeared for the positive health effects of foods, food ingredients, or biochemical compounds derived from several other microalgae, such as Chlorella, Spirulina, Dunaliella, Phaeodactylum, and Pavlova. Until most recently, the prebiotic activity of Euglena and paramylon was reported. Emerging prospects of microalgae as prebiotics were well summarized, but the mechanisms behind the bacterial growth promotion by microalgae are not elucidated yet. Thus, we evaluated the prebiotic prospects of both autotrophic and heterotrophic Euglena on six different Lactobacillus. What’s more, the stimulated mechanism was revealed by bacterial culture medium metabolomic analysis. This study could widen the knowledge about the prebiotic activity of Euglena as a next-generation prebiotic and other microalgae-derived compounds as potential health foods.