We present single molecule fluorescence and spectroelectrochemistry characteristics of 4,4′-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) bearing two carboxylic acid groups at its 2 and 6 positions. Our study shows a heterogeneous half redox potential distribution for the BODIPY molecules embedded in polystyrene film because of the heterogeneity in their charge transfer rates. Single molecules adsorbed onto a TiO₂ surface with ordered nanostructures show surprising fluorescence blinking activity with the shortest ON duration time in comparison to bare glass and indium-tin oxide (ITO) surfaces. Single molecule stability tests show longer ON duration time and a stable fluorescence feature when dispersed in polystyrene thin film than molecules exposed to air. Shorter ON times are observed for molecules. In intimate contact with ITO in comparison to glass substrates. Such a decrease in their fluorescence stability or intensity is explained by charge transfer activities from the dye molecules to the metal oxide surface. Electron transfer and back transfer rates are calculated to illustrate the substrate effects by using a well-established model.