In 2021, 426,309 tons of florfenicol (FCL) were used to control outbreaks of the bacterial pathogen Piscirickettsia salmonis. This antibiotic is administered through medicated food as a metaphylaxis strategy. To date, the effect of this drug on the intestinal epithelia has not been reported in healthy fish. With the objective to study the effect of FCL medicated food at a histological level on the intestinal epithelium, a biological assay with healthy fish was performed. 240 Atlantic Salmon with an average weight of 120 g were divided in three groups were treated by administering feed with different concentrations of FCL. Group 1 (no antibiotic, control); group 2 (20mg/kg FCL); and group 3 (30mg/kg). After transportation to the experimental facilities, the organisms were acclimatized for 30 days. Following the acclimation period, the organism were feed with medicated diets following a prophylactic scheme that is identical to those used in commercial production systems. The applied scheme was the following: 15 days of antibiotic treatment; 10 days off; 15 days of antibiotic treatment; and finally, two following periods of 10 days. At the end of each stage, nine fish from each of the groups were euthanized with an overdose of MS-222. Each specimen was dissected, and a portion of the intestine was taken, fixed with bouin solution and stained with hematoxylin and eosin. We confirmed that fish subjected to the antibiotic treatment had shorter villi and damage in the structure and conformation of the intestinal villi compared to the fish of the control group. These results underscore the importance of optimize antibiotic treatment schemes to mitigate the negative effects associated with current metaphylaxis strategies that undoubtedly affect fish health and welfare.