A pH-driven self-assembly of a simple aza-BODIPY was discovered in PBS solution, whereby ion-specific J-aggregated nanostructures were generated at very low dye concentration (2.5-20 mu M). The aggregation process was investigated in different conditions (pH, temperature and time) by monitoring absorption spectral shifts and associated nanostructure morphological changes. The pH-driven self-assembly process demonstrated an instantaneous thermodynamic phenomenon associated with three characteristic structures, each with distinctive optical properties. When the sample was first formulated within a short time window, a thermodynamically less stable intermediate with an unusual morphology of triangular nanoplates and broad absorption was observed. The formation of these structures was independent of the ions in PBS solution (Na+, K+), thus indicating that the triangular structure was inherent to the anisotropic structure of aza-BODIPY scaffolds. The second structure associated with a metastable pathway generated a uniform population of spherical nanovesicles, while the third structure, generated through a more thermodynamically stable pathway consisted of fibers. The absorption spectra suggested that both spherical and fiber structures contributed to the J-aggregation band at 735 nm in the near infrared optical spectrum and their population in each formulation was concentration dependent. The results highlighted the significance of ion effects in self-assembly of aza-BODIPY and the mechanistic structural changes of the morphology. Furthermore, this fundamental discovery offers a versatile method for the self-assembly of aza-BODIPY J-aggregates as a new nanoplatform with potential photonic applications.