Abstract Excitation‐dependent tuning of the emission behavior of fluorescent organic nanoparticles (FONs) with two simple luminescent pyrenyl–pyridyl conjugates as model systems is demonstrated. In the case of the compound with a flexible bis‐picolyl moiety, the simultaneous presence of multiple ground‐state species with distinct absorption and emission characteristics can be observed. The relative ratios of these species can easily be modulated, and it is possible to selectively stimulate any one of them individually by choosing an appropriate excitation channel. Moreover, at high concentration, a drastic change in the nature of the self‐assembly is observed, which shifts from donor–acceptor‐type self‐assembly to exciplex‐type self‐agglomeration. On the contrary, the compound containing a rigid terpyridine unit has only a single ground state and shows no such tunable emission. However, it can exhibit multiple emission bands in water, whereby the positions of their emission maxima depend on the extent of aggregation‐induced planarization of the probe molecules. Overall, this work demonstrates multimodal modulation of FON emission and a gives insight into how molecular order can translate into complete switching of nanoparticle self‐assembly and photophysics.