The cytoplasmic membrane represents an essential barrier between the cytoplasm and the environment external to cells. Interaction with nanomaterials can alter the integrity of the cytoplasmic membrane through the formation of holes and membrane thinning, which can ultimately lead to adverse biological impacts. Here we use supported lipid bilayers as experimental models for the cytoplasmic membrane to investigate the impact of quantum dots functionalized with the cationic polymer poly(diallyldimethylammonium chloride) (PDDA) on membrane structure. Using a quartz crystal microbalance with dissipation monitoring we show that the positively charged quantum dots attach to and induce structural rearrangement to zwitterionic bilayers in solely the liquid-disordered phase and in those containing phase-segregated liquid-ordered domains. Real-time atomic force microscopy imaging revealed that PDDA-coated quantum dots and, to a lesser extent, PDDA itself induced the disappearance of liquid-ordered domains. We hypothesize this effect is due to an increase in energy per unit area caused by collisions between PDDA-coated quantum dots at the membrane surface. This increase in free energy per area exceeds the approximate free-energy change associated with membrane mixing between the liquid-ordered and liquid disordered phases and results in the destabilization of membrane domains.