Nanoassemblies are formed via self-assembly of ZnS capped CdSe quantum dots (QD) and perylene bisimide dyes (PBI). Upon assembly formation with functionalized dye molecules the QD photoluminescence (PL) is quenched. Quenching has been assigned partly to FRET (fluorescence resonance energy transfer) and NON-FRET processes. By means of time resolved single particle spectroscopy of immobilized QD-dye assemblies, it is demonstrated that NON-FRET processes are due to new non-radiative decay channels caused by the assembly formation process itself. Immobilized (single) assemblies exhibit the same processes as ensembles of assemblies in toluene solution. Only one dye molecule on a QD quenches the PL up to 50%, which is much stronger than is expected when replacing a volume related number of ligands. NON-FRET processes are distinct from photoinduced charge and/or energy transfer. A combination of a Stern-Volmer and FRET analysis of ensemble experiments supports the investigation of the dynamics of assembly formation at extremely low concentration ratios of PBI to QD. This allows us to distinguish between the effects of PBI and ligands on PL quenching on a single molecule level which is not possible in conventional ligand dynamic experiments.