This work verified the antiproliferative and antiproteolytic activities of chlorogenic acid againstRahnella aquatilisKM25, a spoilage organism of raw salmon stored at 4 °C. Chlorogenic acid limited the growth ofR. aqatilisKM25 in vitro at a concentration of 2.0 mg/mL. The dead (46%), viable (25%), and injured (20%) cell subpopulations were identified by flow cytometry following treatment ofR. aquatilisKM25 with the examined agent. The exposure ofR. aquatilisKM25 to chlorogenic acid altered its morphology. Changes in cell dimensions, mostly in length parameters from 0.778 µm to 1.09 µm, were found. The length of untreated cells ranged from 0.958 µm to 1.53 µm. The RT–qPCR experiments revealed changes in the expression of genes responsible for the proliferation and proteolytic activity of cells. Chlorogenic acid caused a significant reduction in the mRNA levels of theftsZ,ftsA,ftsN,tolB,andM4genes (−2.5, −1.5, −2.0, −1.5, and −1.5, respectively). In situ experiments confirmed the potential of chlorogenic acid to limit bacterial growth. A similar effect was noted in samples treated with benzoic acid, where the growth inhibition ofR. aquatilisKM25 was 85–95%. Reduction of microbialR. aquatilisKM25 proliferation significantly limited total volatile base nitrogen (TVB-N) and trimethylamine (TMA-N) formation during storage, extending the shelf life of model products. The TVB-N and TMA-N parameters did not exceed the upper levels of the maximum permissible limit of acceptability. In this work, the TVB-N and TMA-N parameters were 10–25 mg/100 g and 2.5–20.5 mg/100 g, respectively; for samples with benzoic acid-supplemented marinades, the parameters TVB-N and TMA-N were 7.5–25.0 mg/100 g and 2.0–20.0 mg/100 g, respectively. Based on the results of this work, it can be concluded that chlorogenic acid can increase the safety, shelf life, and quality of fishery products.