Multi-walled carbon nanotubes (MWCNTs) can be used as carriers for AgNPs. In the present study, MWCNTs were coated with mesoporous silica for improved delivery of antimicrobial agents. This study also reports a strategy for preparing MWCNTs in which AgNPs are formed in pores using an extract of Angelica gigas Nakai (AGN) prepared by hot-melt extrusion (HME) (HME-AGN) as a reducing agent. Mesoporous silica coating of MWCNTs improved the dispersibility of MWCNTs and induced regular formation of AgNPs. When MWCNTs were decorated with AgNPs and coated with mesoporous silica (MWCNT-AGN), in which the extract was added as a reducing agent, they exhibited increased formation of AgNPs with increasing extract concentration and higher antibacterial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Furthermore, MWCNT-AGN could inhibit biofilm formation known to be involved in the development of antibiotic resistance.