Polyfluorene based conjugated polyelectrolyte/silica nanocomposites are fabricated using sol-gel processing. Ionic termination groups on the conjugated polyelectrolyte lateral chains are shown to control the interaction at the inorganic-organic interface, leading to macroscale homogeneity and nanophase separation in a single material. The extent of nanophase separation is determined by the nature of the ionic groups, which may provide a means of controlling donor-acceptor distances in hybrid systems.