Milk is one of the most widely consumed foods in the world, despite the increasing consumption of plant-based alternatives. Although rich in nutrients and believed by consumers to be free of undesirable contaminants, milk, whether of animal or plant origin, is not always free from residues of chemical substances, including veterinary medicines. For instance, in intensive livestock production, antibiotics are often used to treat animals or, illicitly, to improve their growth performance, which can lead to their presence in the final food. Additionally, the continuous use of veterinary drugs in intensive animal production can lead to their occurrence in agricultural soils and therefore are absorbed by plants as another source of entering the food chain. An effective and accurate multi-detection quantitative screening method to analyze 89 antibiotics in milk was optimized by ultra-high-performance liquid chromatography coupled with a time-of-flight detector (UHPLC-ToF-MS) and further validated in accordance with the Commission Implementing Regulation (CIR) 808/2021 and the International Council for Harmonization (ICH) guidelines on the validation of analytical procedures. Apart from the specific parameters required by CIR 808/2021, the aim was to access the lower limits of the method, limits of detection (LoD) and quantification (LoQ), regardless of the maximum residue limits (MRLs) defined in the legislation. The method was then applied in the analysis of 32 supermarket samples, resulting in four positive findings, including one plant-based sample. The antibiotics found were from the macrolides and sulphonamides families. Nevertheless, the concentrations detected were below the established maximum residue level (MRL).