The extensive use of antibiotics in Chilean salmon farming raises concerns about harmful effects on benthic habitats, particularly the iconic cold-water coral (CWC) banks in semi-enclosed fjords. We collected specimens of the CWC Desmophyllum dianthus near and far from salmon farms in Comau Fjord, Chile, and investigated their associated bacterial community (metabarcoding, culturing) and screened bacterial isolates for their antibiotic resistance (15 antibiotics, including antibiotics common in Chilean salmon farming). The cultured bacterial isolates of D. dianthus showed a slight but significant increase in antibiotic resistance (near: 7.7 ± 0.47 vs. far: 6.3 ± 0.48). This was accompanied by a change in dominance in the randomly selected isolates, with Pseudoalteromonas and Shewanella dominating far and near, respectively. Metabarcoding also showed a shift in the dominant bacterial strains from SUP05 clade to Mycoplasma and a loss of Pseudoalteromonas strains near the salmon farm. Common antibiotics used in salmon farming, however, significantly reduced bacterial growth at the community level, and most bacterial isolates were also sensitive to these antibiotics, except for tilmicosin. This may provide a first indication of how salmon farms modify the microbiome of D. dianthus and underscores the need to expand such assessments in space and time.