The present study was aimed to improve antibacterial and antioxidant impacts of quercetin by making its complex with chitosan (CS-QT) using maleic anhydride as a crosslinker to treat gastroenteritis. CS-QT complex was confirmed by FTIR NMR and TLC studies. Three different types of microspheres i.e., chitosan-polycaprolactone (CS-PCL-Ms), quercetin-polycaprolactone (QT-PCL-Ms), and chitosan-quercetin-polycaprolactone (CS-QT-PCL-Ms) were prepared by ultra-homogenization. Levofloxacin was loaded on these microspheres which were later analyzed by particle size, charge, antioxidant, hemolytic, in-vitro drug release, and antibacterial impact against Pseudomonas aeruginosa 15692, Staphylococcus aureus 12600 and Escherichia coli 25922. In-vivo antidiarrheal model was used to assess histopathological changes along with diarrhea score and weight loss to confirm antibacterial impact of the loaded microspheres. Interestingly antibacterial effect of CS-QT complex and their levofloxacin-loaded microspheres (CS-QT-PCL-Levo-Ms) showed more than two folds increased bactericidal activity against E. Coli and P. Aeruginosa, while 1.5 folds bactericidal against S. Aureus. Similarly, increased antioxidant property of the CS-QT complex was observed due to synergistic properties of chitosan (CS) and quercetin (QT). No skin irritation was shown using 5 µg/100 µL on albino rats by all microspheres. All types of microspheres showed less than 0.5 PDI value and less than 5% hemolytic effect. CS-QT-PCL-Levo-Ms showed less than 50% release in 16 h in phosphate buffer pH 6.8 with first order release behavior. Stability studies revealad approximately 30 months shelf life of CS-QT-PCL-Levo-Ms. CS-QT complex with synergistic antibacterial and antioxidant properties in the form of microspheres can be alternative of the already available antibiotics for the treatment of gastroenteritis.