Facile and convenient carbon dots (CDs) with excellent biocompatibility and strong fluorescence using eco-friendly sources are in high demand for sensing and bioimaging applications. In this study, we used a hydrothermal approach to synthesize highly biocompatible CDs (BCDs) from green fruit vegetables (bottle gourd). By employing the carbodiimide coupling method, these BCDs were functionalized with the tripeptide and phenylboronic acid ligands, glutathione and 4-mercaptophenylboronic acid, respectively. This method enhanced the sensing potential of the nanomaterial for the crucial neurotransmitter, dopamine (DA). These functionalized BCDs (FBCDs) exhibited significant excitation-dependent emission behavior. The BCDs and FBCDs displayed strong blue fluorescence, (λem = 460 nm) and (λem = 458 nm), under excitation wavelengths of 360 and 351 nm, respectively. The FBCDs exhibited an excellent fluorescence quenching response to DA in the wide range of concentrations between 0 and 25 μM and achieved a detection limit of 2.14 μM. The FBCDs were verified as a dual fluorescent probe by demonstrating in vitro detection of DA in SH-SY5Y (human neuroblastoma) cells. The FBCDs also enabled superior bioimaging in SH-SY5Y cells via multi-color emissions, including of blue, green, and red. The practicality of the proposed FBCDs was also investigated in human serum.