The aim of this study was to investigate a method of embedding l‐cysteine (l‐cys), an antimicrobial agent, between layers of chitosan (CH) and sodium alginate (ALG) onto cotton samples obtained via a layer‐by‐layer electrostatic deposition technique via several embedding methods. The results show that the best way to incorporate l‐cys into the layers was the one that used the property of gelling ALG. To monitor the l‐cys embedding into the CH/ALG multilayer film, different methods were used: energy‐dispersive X‐ray spectrometry analysis to assess the presence of sulfur on the sample, Ellman's reagent method to analyze l‐cys release from the sample, and attenuated total reflectance (ATR) Fourier transform infrared spectroscopy (FTIR) to compare the ATR–FTIR spectra of the pure l‐cys and l‐cys embedded in the CH/ALG multilayer film to study the interaction between the l‐cys and the CH/ALG multilayer films. Functionalized CH/ALG cotton samples were also investigated for their antibacterial properties toward Staphylococcus aureus and Klebsiella pneumonia with the Japanese Industrial Standard method JIS L 1902:2002, and the results show an enhancement of the antibacterial effect due to the presence of l‐cys. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40519.