Fluorescent zinc complexes of 1,2-disubstituted benzimidazole (R1–R3) have been synthesized and characterized using single crystal X-ray diffraction. The ligands L1–3 were found to be less emissive due to photoinduced electron transfer (PET) mechanism originated from the electron pair of benzimidazole nitrogen. The complexation of ligands with Zn(II) not only enhances the fluorescent intensity; it also orients the ligands to a new packing. It was observed that the aromatic unit plays a decisive role in the packing of the molecules. The complex R1 has extended the coordination through C–H···π interaction, whereas complex R2 involved C–H···π interaction and C–H···Br interaction for packing in supramolecular architecture. Among these complexes, R3 showed the most interesting noncovalent interaction pattern involving C–H···π interaction, C–H···Br interaction, and π–π stacking between pyrene rings. These noncovalent interactions govern photophysical properties that are sensitive toward the microenvironment. Thus, by altering these interactions, the selective sensing for a particular analyte can be achieved. The complexes R1 and R2 have shown enhanced emission intensity upon interacting with adenosine triphosphate (ATP) competitively in the presence of some other tested anions. A ratiometric change in emission spectra of the complex R3 was observed upon binding with ATP in semiaqueous medium offering the lowest detection limit of 15 nM. Upon interaction with ATP, the π–π stacking between pyrene rings breaks and results in a decrease in excimer emission at 470 nm and increases in monomeric emission intensity at 410 nm. The AFM (Atomic force microscopy) images of receptor R3 show that upon addition of ATP to the R3 solution, solvent mediated aggregation takes place, which results in the ratiometric detection. In the dimethylformamide solvent system, aggregates were formed, whereas in a water/tetrahydrofuran solvent system the clear solution was converted to a highly viscous gel. To investigate the applications of the prepared sensor, the fluorescence response of HeLa cells enriched with ATP was observed using fluorescence microscopy. The fluorescence modulation of the sensor in living cells makes the receptor practically applicable in a biological environment. Quantitative analysis of apyrase activity has shown that the presented sensor R3 is capable of monitoring the hydrolysis process in the biological system.