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<i>Piscirickettsia salmonis</i> is the pathogen that most affects the salmon industry in Chile. Large quantities of antibiotics have been used to control it. In search of alternatives, we have developed [Cu(NN₁)₂]ClO₄ where NN₁ = 6-((quinolin-2-ylmethylene)amino)-2H-chromen-2-one. The antibacterial capacity of [Cu(NN₁)₂]ClO₄ was determined. Subsequently, the effect of the administration of [Cu(NN₁)₂]ClO₄ on the growth of <i>S. salar</i>, modulation of the immune system and the intestinal microbiota was studied. Finally, the ability to protect against a challenge with <i>P. salmonis</i> was evaluated. The results obtained showed that the compound has an MIC between 15 and 33.9 μg/mL in four isolates. On the other hand, the compound did not affect the growth of the fish; however, an increase in the transcript levels of IFN-γ, IL-12, IL-1β, CD4, lysozyme and perforin was observed in fish treated with 40 μg/g of fish. Furthermore, modulation of the intestinal microbiota was observed, increasing the genera of beneficial bacteria such as <i>Lactobacillus</i> and <i>Bacillus</i> as well as potential pathogens such as <i>Vibrio</i> and <i>Piscirickettsia</i>. Finally, the treatment increased survival in fish challenged with <i>P. salmonis</i> by more than 60%. These results demonstrate that the compound is capable of protecting fish against <i>P. salmonis</i>, probably by modulating the immune system and the composition of the intestinal microbiota.