Co-infection of malaria and bacterial pathogens poses a major threat to public health, particularly in regions with high malaria endemicity and limited antibiotic stewardship. This study investigated the multiple antibiotic resistance (MAR) patterns and Extended-Spectrum Beta-Lactamase (ESBL) gene distribution of bacterial isolates from the blood of malaria patients attending government hospitals in Ondo State, Nigeria. Blood samples from malaria-confirmed patients were cultured for bacterial isolation and identification using standard microbiological techniques. The antibiotic susceptibility of isolates was determined by the Kirby–Bauer disc diffusion method. Multiple antibiotic resistance phenotypes and MAR indices were calculated. ESBL production was detected phenotypically and genotypically using PCR. Plasmid extraction and curing were performed to determine the role of plasmids in resistance dissemination. Bacterial isolates exhibited high resistance to amoxicillin (96.52%), cefuroxime (89.57%), chloramphenicol (86.09%), and tetracycline (83.48%), but showed low resistance to ofloxacin (16.52%) and gentamicin (24.35%). Enterobacter aerogens, Pseudomonas aeruginosa, and Shigella dysenteriae displayed complete resistance (100%) to several antibiotics, including amoxicillin and chloramphenicol. A total of 34 multiple antibiotic-resistant (MAR) phenotypes were recorded, with the predominant pattern being AUG–CRX–TET–CH–S–AMX, observed in E. coli, S. Typhi and S. enteritidis. The most frequent MAR indices were 0.625 (22.61%) and 0.75 (21.74%). Phenotypic detection revealed ESBL occurrence rates of 66.09%, 31.30%, and 33.91% using disc diffusion, approximation, and combination methods, respectively. Genotypically, the prevalences of bla TEM, SHV and CTX-M genes were 12.82%, 12.82%, and 33.33%, respectively, with E. coli and S. Typhi being the dominant carriers. Plasmid sizes ranged from 2 to 80 kbp, with some isolates harboring multiple plasmids. Post-curing analysis showed loss of resistance in most isolates, confirming plasmid-mediated resistance in several strains. This study highlights the alarming prevalence of multidrug-resistant and ESBL-producing bacteria among malaria patients in Ondo State, Nigeria. The detection of plasmid-mediated resistance underscores the urgent need for rational antibiotic use, continuous surveillance, and infection control strategies to mitigate antimicrobial resistance in malaria-endemic regions.