Through developing a highly efficient solid-phase microwave-assisted (SPMA) synthesis technique, we were able to synthesize graphene quantum dots (GQDs) that were doped with nitrogen and boron atoms. The as-synthesized GQDs were employed as sensing probes for detecting pesticides and iron ions within aqueous solutions. The SPMA approach is very versatile for in-situ doping of multiple atoms within the graphitic structure of GQDs. The maximal B/C and N/C atomic ratios within the GQD structures were reached as high as 28.6 and 86.4 at.%, respectively. For the B-/N-codoped GQDs, the N dopants comprises of pyrrolic/pyridinic N and graphitic N, whereas the B doping mainly involves two bonding types (i.e., B4C and BCO2) inserted into or decorated on the GQD skeleton structure. Based on the analysis of the Stern-Volmer plots, the B-/N-codoped GQDs can be employed as probing nanomaterials toward Fe2+ and paraquat detection thanks to their incredible sensitivity throughout the photoluminescent quenching. The PL quenching mechanism of GQDs is usually governed by the GQD‒(paraquat)x intermediates formation and the resulting π–π stacking that can easily quench and aggregate. The findings of this work pave the pathway to engineering the chemical compositions as well as the crystalline structures of GQDs, used for energy and other sensing devices.