Three batches of yoghurts were made from goat's milk with different enrofloxacin concentrations (0, 50, 100 and 150 μg/kg). Quality parameters were analysed at 1, 7, 14 and 28 days at 5 °C. Drug residues were also quantified by HPLC. Coagulation time and most yoghurt properties remained unaffected by the presence of enrofloxacin in goat's milk. However, quality parameters were affected by the storage period. 74.9–99.2% of enrofloxacin initially added to goat's milk remained in the yoghurt throughout its entire shelf life, potentially posing a risk to consumer health. Therefore, an enrofloxacin maximum residue limit in yoghurt should be established.