Commensal Escherichia coli in livestock represent important reservoirs of antimicrobial resistance (AMR) and virulence determinants with potential zoonotic implications. However, genomic data integrating phenotypic resistance and whole-genome characterization of bovine-derived E. coli in Bangladesh remain limited. This study investigated the prevalence, antimicrobial susceptibility, and genomic characteristics of E. coli isolated from bovine fecal samples collected across three districts of Bangladesh. A total of 92 samples were processed using culture-based identification and biochemical tests, followed by molecular confirmation via 16S rRNA gene sequencing and phylogenetic analysis. Antimicrobial susceptibility testing was conducted using the Kirby–Bauer disk diffusion method. Whole-genome sequencing of a representative isolate was performed using Illumina technology, followed by de novo assembly, annotation, virulence gene detection, plasmid profiling, and in silico multilocus sequence typing (MLST). E. coli was detected in 45 samples (48.91%), with variable prevalence across locations. Molecular confirmation showed ≥ 99% sequence identity with reference strains. Antimicrobial susceptibility testing revealed high resistance to amoxicillin, cefradine, and clotrimazole, while susceptibility remained high for imipenem and ceftriaxone. Multidrug resistance was observed in 77.7% of isolates, and 75% exhibited MAR index values > 0.2. Whole-genome sequencing produced a 7.79 Mb assembly containing 7,218 coding sequences and identified multiple virulence genes (iss, astA, lpfA, air, and eilA) and IncF-family plasmid replicons (IncFIC, IncFIA, IncFIB, ColRNAI). MLST analysis indicated previously unassigned sequence types. Commensal bovine E. coli in Bangladesh harbor multidrug resistance traits, virulence-associated genes, and mobile plasmids that may facilitate zoonotic transmission and resistance dissemination. These findings provide baseline genomic surveillance data and highlight the need for integrated antimicrobial stewardship and One Health monitoring strategies in livestock systems.