The identification of novel sources of synbiotic agents with desirable functionality is an emerging concept. In the present study, novel encapsulates containing probiotic L. acidophilus LA-05® (LA) and Charantin (CT) were produced by freeze-drying technique using pure Whey Protein Isolate (WPI), pure Maltodextrin (MD), and their combination (WPI + MD) in 1:1 core ratio, respectively. The obtained microparticles, namely WPI + LA + CT, MD + LA + CT, and WPI + MD + LA + CT were tested for their physicochemical properties. Among all formulations, combined carriers (WPI + MD) exhibited the highest encapsulation yields for LA (98%) and CT (75%). Microparticles showed a mean d (4, 3) ranging from 50.393 ± 1.26 to 68.412 ± 3.22 μm. The Scanning Electron Microscopy revealed uniformly amorphous and glass-like structures, with a noticeably reduced porosity when materials were combined. In addition, Fourier Transform Infrared spectroscopy highlighted the formation of strong hydrogen bonds supporting the interactions between the carrier materials (WPI and MD) and CT. In addition, the thermal stability of the combined WPI + MD was superior to that of pure WPI and pure MD, as depicted by the Thermogravimetric and Differential Scanning Calorimetry analysis. More interestingly, co-encapsulation with CT enhanced LA viability (8.91 ± 0.3 log CFU/g) and Cells Surface Hydrophobicity (82%) in vitro, in a prebiotic-like manner. Correspondingly, CT content was heightened when co-encapsulated with LA. Besides, WPI + MD + LA + CT microparticles exhibited higher antioxidant activity (79%), α-amylase inhibitory activity (83%), and lipase inhibitory activity (68%) than single carrier ones. Furthermore, LA viable count (7.95 ± 0.1 log CFU/g) and CT content (78%) were the highest in the blended carrier materials after 30 days of storage at 4 °C. Synbiotic microparticle WPI + MD + LA + CT represents an effective and promising approach for the co-delivery of probiotic culture and bioactive compounds in the digestive tract, with enhanced functionality and storage properties.