A non-thermal, high density atmospheric plasma glow discharge treatment was used to impart functionality to cotton/polyethylene terephthalate (PET) fabric to furnish a surface that is water repellent and then antimicrobial only. In this work, cotton/PET (50/50%) blend fabric was treated with a water repellent treatment through activating the surface with plasma, depositing a vaporized fluorocarbon based monomers, 1,1,2,2-tetrahydroperfluorodecyl acrylate (THPFDA) and 1,1,2,2-tetrahydroperfluorododecyl acrylate (THPFDDA), then graft polymerizing the monomer with a second plasma exposure. Samples were then further treated with an antimicrobial agent, diallyldimethylammonium chloride (DADMAC), a quaternary ammonium salt. Plasma treatment was used to induce free radical chain polymerization of the DADMAC, conferring a graft polymerized network on the fabric with potentially durable antimicrobial properties. It was shown that the water repellent treatment via plasma induced-graft polymerization was successful in yielding a highly hydrophobic fabric with a finish durable to laundering. The results of the antimicrobial tests showed that the treated fabric reduced the activity of both gram positive and gram negative bacteria by more than 99.994%, demonstrating that the antimicrobial agent can function effectively on the water repellent treated fabric. However, despite the evidence of the presence of fluorine containing compounds on the fabric following the antimicrobial treatment, which was confirmed by time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis, the water repellency was lost, which was attributed to changes in the orientation of the fluorocarbon polymer chains.