Quaternary ammonium salts and N-halamines are widely used as biocides in antimicrobial coatings, and have been extensively studied over the past two decades. In this work, 5,5-dimethyl-3-(3′-triethoxysilylpropyl)hydantoin (SPH), and 3-(trimethoxysilylpropyl) octadecyl dimethyl ammonium chloride (SPODA) were synthesized and coated onto cotton fibers using a pad-dry process (PD) and the traditional pad-dry-cure process (PDC). The coated cotton swatches were characterized by FT-IR and SEM. The quaternary ammonium salt showed a relatively lower inactivating bacteria efficacy than did the N-halamine compounds. The chlorinated swatches coated with both SPH and SPODA using the PD process could inactivate about 7 logs of the Staphylococci aureus within 5–10 min and 7 logs of Escherichia coli O157:H7 within 10–30 min, respectively. The addition of quats in N-halamine coatings improved antimicrobial activity against Gram-negative bacteria E. coli O157:H7. However, this result was not observed when the PDC process was applied in coatings because of the increasing hydrophobicity of the coated samples under high coating temperature.