Phenanthroline-based chiral ligands L(1) and L(2) as well as the corresponding Eu(III) and Tb(III) complexes were synthesized and characterized. The coordination compounds show red and green emission, which was explored for the sensing of a series of anions such as F(-), Cl(-), Br(-), I(-), NO3(-), NO2(-), HPO4(2-), HSO4(-), CH3COO(-), and HCO3(-). Among the anions, HPO4(2-) exhibited a strong response in the emission property of both europium(III) and terbium(III) complexes. The complexes showed interactions with the nucleoside phosphates adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP). Owing to this recognition, these complexes have been applied as staining agents in the microalgal cell Chlorella vulgaris. The stained microalgal cells were monitored through fluorescence microscopy and scanning electron microscopy. Initially, the complexes bind to the outer cell wall and then enter the cell wall through holes in which they probably bind to phospholipids. This leads to a quenching of the luminescence properties.