The development of carbon dots (CDs) as a facile high luminescent sensor for the detection of heavy metal ions is gaining more attention due to their excellent optical properties and inherent non-toxic nature. Herein, we developed nitrogen-doped carbon dots (N-CDs) using a single-step rapid microwave technique by employing citric acid with L-glutamine followed by boron functionalization using boric acid for the synthesis of boron-nitrogen doped carbon dots (BN-CDs) by using reflux reaction condition. These BN-CDs exhibited outstanding photo-stability, excellent aqueous dispersibility, low cytotoxicity, and high photoluminescence quantum yield (QY) of ∼ 21.9 ± 2.7 % and emitted green fluorescence under UV light. BN-CDs were found to display photoluminescence quenching very specific towards auric ions (Au3+ ions) with a detection limit of 3.1 ± 0.45 nM. The quenching observed in the detection process was primarily due to coordination-induced aggregation mechanism. Moreover, BN-CDs were also found to have superior radical scavenging activity, excellent cytocompatibility and cell imaging properties. Thus, prepared BN-CDs can have potential applications in the accurate detection of auric ions as well as in cell imaging applications.