Near infrared (NIR) fluorescence imaging is a striking imaging modality for biomedical and clinical applications due to its deep tissue penetration and low phototoxicity. The major issue with NIR dyes is their non-specific distribution and requirement of tagging with biomolecules for specific tissue localization. Till now, there have been no imaging agents available that can distribute into a specific organ without the need for targeted ligands, which remains as an unmet clinical need. In the present study, we demonstrate that the Zinnia elegans plant extract (abbreviated as ZE) assisted synthesis of highly biocompatible gold nanoparticles (AuZE), leading to their non-invasive bio-imaging applications in the NIR region (red at 820 nm emission: NIR region). AuZE and ZE both exhibited green fluorescence at 350 nm excitation and red fluorescence in the NIR region (710 nm). We verified the source of this fluorescence, which originates from the fluorescent molecules present in the ZE extract. After intraperitoneal administration in C57BL6 mice, very interestingly, AuZE is distributed into the brain of C57BL6 mice without the need for any targeted ligand and exhibited bright red fluorescence in the NIR region (710 nm excitation, 820 nm emission) as evidenced by non-invasive imaging as well as ICPOES techniques. We further explored the activity of ZE and AuZE as cell labeling agents (B16F10 cells were pre-incubated with AuZE and implanted into mice, and the fluorescence was monitored), which could be applicable for graft transplantation biology. To the best of our knowledge, this is the first report that demonstrates the versatile applications of green synthesized gold nanoparticles using a ZE extract. Considering these exciting results and fruitful outcomes, the ZE and AuZE NPs would stand as an alternative imaging agent to commercially available NIR dyes and change the conventional fluorescence-based bioimaging strategies. Therefore, the biosynthesized AuNPs open new directions for future research to explore these latest observations in the field of disease diagnosis and therapy.