Chitosan/clay (nano)composites were prepared by using a special quaternary ammonium intercalating agent coupled with a silanol group to facilitate the organic clay formation. Exfoliated clay in the chitosan matrix was attained at the higher intercalant dosages through X-ray diffraction (XRD) and transmission electron microscope (TEM) analyses. Optical transmittance for the (nano)composites increased slightly with increasing the amount of intercalants in the clays. In light of the hydrophobic component on the intercalant and the effective clay content, the interfacial interaction between chitosan and modified clay may not be strong enough to render higher mechanical properties, even though the partially exfoliated clays were achieved to provide high interfacial area for the dispersed phase and the matrix. An optimum Young’s modulus was thus found for (nano)composites using modified clay at a medium dosage of intercalant, which resulted from the balance of the dispersion status and interfacial interaction. This outcome indicated high dispersion of modified clay may not guarantee high mechanical properties of (nano)composites. The antimicrobial property of chitosan against Escherichia coli (E. coli) increased further with the addition of modified clays, in which the intercalant exhibiting the antimicrobial function. The modified clay at an optimum dosage of modifier to balance the mechanical properties and antimicrobial property was attained.