Oral health is essential for general well-being, and mouthwash is a popular technique of plaque reduction. Shrimp shell-derived chitosan has the potential for use in oral healthcare. The objective of this work was to prepare chitosan from prawn shells, assess its production efficiency, and antimicrobial properties. The efficiency of a seafood-derived chitosan mouthwash in reducing Streptococcus mutans, Lactobacillus acidophilus, and plaque development was also investigated. Chitosan was prepared from shrimp shells using a modified industrial method and analyzed through protein concentration measurements, thermogravimetric/differential thermal analysis (TG/DTA), and Fourier-transform infrared spectroscopy (FTIR). The minimal inhibitory concentration (MIC) of chitosan against S. mutans was determined. A 2% chitosan solution showed in vitro inhibition of S. mutans and L. acidophilus. Twenty healthy volunteers (aged 18–25) were divided into control (commercial mouthwash) and treatment (chitosan mouthwash) groups. Saliva and plaque samples were collected before and after a 14-day rinsing regimen, and bacterial counts were statistically analyzed. The chitosan yields after deproteinization, demineralization, and deacetylation were 83 ± 10%, 68 ± 8%, 53 ± 9%, respectively. Deproteinization was completed within 5-10 hours. Thermogravimetric/differential thermal analysis (TG/DTA) revealed decomposition temperatures of 263.05°C after deproteinization and deacetylation, and 303.86°C after the combined deproteinization, demineralization, and deacetylation process. The corresponding weight losses were 47.11% and 84.88%, respectively. FTIR analysis confirmed that the chemical properties of the produced chitosan were comparable to those reported in previous studies. Both commercial and chitosan-based mouthwashes demonstrated antibacterial and antiplaque properties. The chitosan mouthwash was effective against S. mutans, reducing its population by 29.2% compared to 3.6% with the commercial mouthwash. Both mouthwashes reduced L. acidophilus populations (commercial: 68.8%, chitosan: 51.2%), though the difference was not significant. Chitosan can be efficiently extracted from shrimp shells using a modified industrial method. The 2% chitosan mouthwash demonstrated superior antimicrobial activity against S. mutans, highlighting its potential as an effective tool in oral healthcare.