Antimicrobial surfaces are needed for many health care applications. Single walled carbon nanotubes (SWNT) have shown promise as antimicrobial agents, but important questions persist concerning the effects of tube bundling, a common phenomenon owing to strong hydrophobicity. We investigate here the influence of bundling on the layer-by-layer (LbL) assembly of SWNT with charged polymers, and on the antimicrobial properties of the resultant films. We employ a poly(ethylene glycol) functionalized phospholipid (PL-PEG) to disperse SWNT in aqueous solution, and consider cases where SWNT are dispersed (i) as essentially isolated objects and (ii) as small bundles. Quartz crystal microgravimetry with dissipation (QCMD) and ellipsometry measurements show the bundled SWNT system to adsorb in an unusually strong fashion – with layers twice (when hydrated) and three times (when dried) as thick as those of isolated SWNT. Molecular dynamics simulation reveals a lower PL-PEG density and degree of solution extension on bundled versus isolated SWNT, suggesting thicker adsorbed layers may result from suppressed steric repulsion between bundled nanotubes. Enhanced van der Waals attraction in the bundled system may also play a role. Scanning electron micrographs reveal Escherichia coli on films with bundled SWNT to be essentially engulfed by the nanotubes, whereas the bacteria rest upon films with isolated SWNT. While both systems inactivate 90% of bacteria in 24 h, the bundled SWNT system is “fast-acting,” reaching this inactivation rate in 1 h. This study demonstrates the significant impact of SWNT bundling on LbL assembly and antimicrobial activity, explores the molecular basis of nanotube–nanotube interactions, and demonstrates the possibility of bacteria-engulfing, fast-acting, SWNT-based antimicrobial coatings.