Antimicrobial resistance (AMR) is rising globally and is likely to cause more deaths because of antibiotic-resistant microbial infections and antibiotic residues in animal foods and products as a result of misuse of antibiotics in dairying. Thus, we determined the presence and quantities of sulfonamide, tetracycline, and beta-lactam drug residues in milk sampled in Nyandarua, Meru, and Kiambu counties in Kenya using the Charm TRIO® test kit and liquid chromatography (LC) coupled to the triple quadrupole mass spectroscopy (MS) (LC-MS/MS). The TRIO® test kit showed dicloxacillin as the most prevalent at 9.3%, followed by penicillin and cloxacillin at 3.7% each, and nafcillin at 0.9% among the beta-lactams. Among the tetracyclines, demeclocycline and tigecycline were the most prevalent at 10.3% each, followed by oxytetracycline at 9.3%, chlortetracycline at 7.5%, and doxycycline at 3.7%, while sulfaquinoxaline was the only sulfonamide drug detected at 4%. The LC-MS/MS detected the presence of all the tested β-lactam and tetracycline antimicrobial traces and all sulfonamide drugs except sulfamerazine in all three counties. All the tetracycline antibiotics recorded between 3 and 10.5% of antibiotic residues above the recommended Maximum Residue Levels (MRLs) in milk across all three counties, with beta-lactam antibiotics recording between 2 and 33.3%, indicating their misuse in the three counties. Sulfaquinoxaline was the only sulfonamide detected in milk samples above the recommended MRLs, indicating sulfonamides are less used in those counties. Therefore, it is important to enforce a regulatory framework to control antibiotic use in livestock to minimize potential health risks related to their traces in the foods.