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This study aims to detect <i>Clostridium botulinum</i> and its control using natural leaf extracts of <i>Citrus limon</i>, <i>Citrus sinensis</i>, and <i>Citrus unshiu</i> in Egyptian fish products, e.g., canned tuna, canned sardine, canned mackerel, fesikh, moloha, and renga, as well the application of <i>C. limon</i> in tuna. Moreover, the antibacterial activity of the <i>C. limon</i> leaf extract was also estimated. In the water extract, ascorbic acid, total flavonoid content (TFC), and total phenolic content (TPC) were determined by volumetric, aluminum chloride, and Folin–Ciocalteu approaches, respectively. The antioxidant ability of the extract was analyzed in vitro via free radical scavenging (DPPH) and Ferric reducing assays. The results showed variability in the distribution of the total number of positive <i>C. botulinum</i> in fish samples from three different governorates under study, which were (24) Alexandria, (16) Beheira, and (17) Gharbia, out of the 120 tested samples in each governorate. Additionally, the findings revealed that all three <i>Citrus</i> extracts contain an appropriate number of secondary metabolites, with a sustainable presence of saponin and tannins in the <i>C. limon</i> extract. Furthermore, all <i>Citrus</i> extracts inhibited bacterial growth by increasing the inhibition zone, with <i>C. limon</i> being the best extract (25 mm) compared to <i>C. sinensis</i> and <i>C. unshiu</i>. The overall results showed the high antioxidant and anti-<i>Clostridium</i> powers (<i>p</i> < 0.05) of <i>C. limon</i> leaf extract, indicating its preservative activity in fishery products during storage. Finally, <i>C. limon</i> leaf extract can fight off <i>C. botulinum</i> and is considered a promising natural preservation candidate in ensuring safe and fresh fishery products.