Background/Objectives: This study characterized the phenotypic and genotypic profiles of antimicrobial resistance in 104 Escherichia coli isolates obtained from 22 samples of artisanal Minas Frescal cheese from the Federal District, Brazil. Methods: The antimicrobial susceptibility of E. coli isolates was assessed using the disk diffusion method and antimicrobial resistance genes were detected using polymerase chain reaction methods with specific primers. Results: The highest rates of phenotypic antimicrobial resistance were observed for sulfonamides (85.58%, 89/104) and tetracyclines (38.46%, 40/104). In the genotypic profiles, most E. coli isolates carried the sulfonamide resistance genes sul1/sul2 (62.50%, 65/104), tetracycline resistance genes tetA/tetB (65.38%, 68/104), and β-lactam resistance genes blaCTX-M/blaTEM/blaSHV (55.77%, 58/104). Most E. coli strains that presented sulfonamide resistance genes carried the sul1 gene (49.04%, 51/104) and were phenotypically sulfonamide-resistant strains (59.61%, 62/104). Regarding the E. coli strains that carried tetracycline resistance genes, the majority harbored both tetA and tetB genes (34.61%, 36/104), with 35.56% (37/104) being phenotypically resistant and 29.80% (31/104) being phenotypically susceptible. For E. coli strains that presented β-lactam resistance genes, the most frequently detected gene was blaCTX-M (21.15%, 22/104) and, notably, most E. coli strains (43.26%, 45/104) were phenotypically susceptible. The cat1 and clmA genes (associated with phenicol resistance) were detected in 22.12% of the E. coli isolates (23/104), with only two strains (1.92%) being phenotypically resistant to chloramphenicol. Conclusion: The high prevalence of E. coli carrying antimicrobial resistance genes in artisanal cheese raises public health concerns regarding the dissemination of potentially pathogenic antimicrobial-resistant microorganisms through the food chain.