Fluorescent atacamite nanoclusters (FANCs) have been developed and modified with silica for Drosophila salivary gland tissue imaging and photothermally induced cell death of osteosarcoma MG-63 cells. FANCs were synthesized with Moringa oleifera leaf extract without using any hazardous reducing and external capping agents. FANC was further used to evaluate light absorption, fluorescence emission, band gap, and magnetic properties as the first report on such nanoclusters. Upon excitation with a 350 nm light source, FANCs exhibited fluorescence at 460 nm, with a relative quantum yield of 0.3%. Besides, silica-encapsulated fluorescent atacamite nanoclusters (SEFANC) manifested remarkable improvement in emission, quantum yield (1.7%), shelf-life (15 d), biocompatibility, and photostability. Concomitantly, it has also increased the absorption in the near-infrared region and demonstrated high heat generation potential (42 °C → 50 °C). The above results suggest that FANC can be a potential candidate in the area of nanomedicine for a number of applications such as bioimaging, photothermal therapy, etc.