Antimicrobials are administered in livestock for different uses leading to milk contamination and several undesirable effects. Because there is a lack of surveillance of antimicrobial residues (AMRs) in milk and dairy products in Lebanon, this study aims to determine the occurrence of AMRs in 90 Lebanese samples of milk and labneh (concentrated yoghurt). Multi-residue screening methods with suitable sample preparations were applied to detect 71 AMRs in milk and labneh, respectively, using LC-MS/MS. Of the total number of samples, 71% was contaminated with AMRs and (fluoro)quinolones and macrolides were the most detected families. Additional confirmation tests proved that 6.7% of the milk samples were non-compliant for the macrolides tilmicosin, tulathromycin and spiramycin. Moreover, some labneh prepared from contaminated milk samples was analysed to determine the fate of AMRs during the manufacturing process. The results showed that some AMRs could be concentrated, eliminated or degraded, based on their physicochemical characteristics.