Silver colloidal nanoaggregates have been widely used for surface‐enhanced Raman scattering (SERS) measurements. SERS‐active nanoaggregates generally show monotone colors, although multicoloured‐blinking emissions, which occur at the single‐molecule level, have been observed from each Ag colloidal nanoaggregate with poly‐L‐lysine. For the same single nanoaggregates, SERS peaks of poly‐L‐lysine were observed at shorter wavelengths than those of the background emission band; thus, their blinking can be measured separately. The background emission is attributed to fluorescence from an Ag atomic cluster. This may be modulated by the surface plasmon enhancement of each Ag nanoaggregate and is the likely cause of multicoloured background emission. Notably, the probability distributions as a function of time for not only the dark events of SERS but also those of the background emission were reproduced via a truncated power law, indicating the same random‐walk mechanism for their blinking despite the different illuminants. The power law for the dark background emission events was truncated at a shorter tail than that for the dark SERS events. This result suggests that the fluorescent Ag cluster reaches a junction of the Ag nanoaggregate covered with citrate anions more quickly than the cationic polymer chain. Copyright © 2017 John Wiley & Sons, Ltd.