Pomegranate flower extract, rich in anthocyanins, demonstrates beneficial health-promoting properties such as an anti-diabetic and antioxidant effect, among others. However, the potential health-promoting properties may be hindered by the low stability of anthocyanins. Therefore, the aim of our study was to assess whether stabilizing carriers, namely HP-γ-cyclodextrin (HP-γ-CD), α-cyclodextrin (α-CD), Methyl-β-cyclodextrin (Me-β-CD), Inulin (Inu) and Arabic gum (AGu) affect the antioxidant and antidiabetic activity of lyophilized pomegranate flower extract, how they influence stability, release profile, and whether the systems exhibit prebiotic activity. Interactions between pomegranate flower extract and these factors were analyzed using FT-IR. The structures were examined through microscopic imaging while for the prepared prebiotic systems, antidiabetic activity was determined and confirmed by the inhibition of α-amylase and α-glucosidase; antioxidant activity was expressed by DPPH and CUPRAC assays. The content of pelargonidin-3,5-glucoside in these systems was assessed using the HPLC method. The release profiles of pelargonidin-3,5-glucoside were examined in a medium at pH = 6.8 and pH = 1.2, and the stability was assessed after subjecting the systems to high temperatures (T = 90 °C). The prebiotic potential was evaluated for 10 prebiotic bacterial strains (Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus brevis Lactobacillus rhamnosus gg, Lactobacillus reuteri, Pediococcus pentosaceus, Lactococcus lactis, Lactobacillus fermentum lf, Streptococcus thermophilus). As a result of the conducted research, better functionalities of the obtained systems containing Pomegranate flower extract were proven in terms of prebiotic and antidiabetic effects. The obtained delivery systems for pelargonidin-3,5-glucoside allow for better use of its health-promoting effects.