Urinary tract infections (UTIs) caused by pathogens, particularly E. coli, have spontaneously become resistant to antimicrobial drugs in recent years. Therefore, regular monitoring and alternative strategies for the antimicrobial agent are crucial for combating antimicrobial resistance and bacterial biofilms. Here, we report a new cobalt iron oxide-conjugated tin oxide nanocomposite that can kill bacteria and treat multidrug-resistant E. coli posing UTIs. Following the isolation and identification of E. coli, we tested 57/134 samples against sixteen commonly used antibiotics phenotypically using the disk diffusion method to determine their sensitivity pattern. Of the 57 E. coli isolates, 66% (38/57) were multidrug-resistant. The E. coli isolates were resistant to cephradine (70.17%), ceftriaxone (59.64%), and azithromycin (59.64%), followed by cefixime (54.38%), cefuroxime sodium (52.63%), and co-trimoxazole (50.87%). X-ray diffraction results showed the crystallite sizes were about 5.68 and 8.84 nm in pure SnO2 nanoparticles and 95% SnO2-5% CoFe2O4 nanocomposite, respectively. Energy-dispersive X-ray spectroscopy and Fourier transform infrared determined the fundamental structure of the nanocomposite, encompassing Co, Fe, Sn, and O. Moreover, FTIR measurements implied that the distinct functional groups in both SnO2 and CoFe2O4 nanoparticles existed in a 95% SnO2-5% CoFe2O4 nanocomposite. Field emission scanning electron microscope analysis uncovered that the SnO2-CoFe2O4 nanocomposite had a size of roughly 24 nm and was spherical. In addition, the biosynthesized SnO2 nanoparticles and SnO2-CoFe2O4 nanocomposite were evaluated for their antibacterial activity. At a minimum 100 µg/mL concentration, SnO2 nanoparticles and SnO2-CoFe2O4 nanocomposite showed high antibacterial activity. The SnO2 nanoparticles and SnO2-CoFe2O4 nanocomposite demonstrated antibacterial activity on multidrug-resistant E. coli at 10 ± 0.7 and 16 ± 0.8 mm zone of inhibition, respectively. In conclusion, the new SnO2-CoFe2O4 nanocomposite might be a potential candidate for treating UTIs caused by drug-resistant E. coli in the foreseeable future.