Anionic polygalacturonic acid (PGA), a prebiotic for healthy microbiota, and cationic polyethyleneimine (PEI), a strong antimicrobial polymer against harmful infections, were ionically crosslinked to prepare biocompatible and antibacterial polygalacturonic acid/polyethyleneimine (PGA/PEI) polyplex particles. The PGA/PEI particles were spherical in shape and had a wrinkled surface with a micron size range of particles from 9 to 0.6 μm. The PGA/PEI polyplex particle was degradable under more acidic and basic conditions but was highly stable between pH 3 and 7. The prepared PGA/PEI polyplex particles are found compatible for intravenous applications with hemolysis rate of less than 1% and almost 100% blood clotting index values up to 1 mg/mL concentration. Similarly, no significant toxicity was found on L929 fibroblast cells for 24 h incubation time in the presence of 1 mg/mL concentration of the PGA/PEI polyplex particles. As an antibacterial material, the PGA/PEI polyplex particles totally prevented the growth of Gram‐negative Escherichia coli and Gram‐positive Staphylococcus aureus. Due to the antibacterial, biocompatible, blood compatibility, and degradability, the PGA/PEI polyplex particles can be utilized in wide range of application such as particularly wound dressing, cosmetic and health care products, and drug delivery applications.