Zero-dimensional graphene quantum dots have attractive properties but the synthesis of graphene quantum dots in a simple and scalable technique is tedious, which limits its utilization in different energy storage application. In this study, we present a simple and scalable approach to produce graphene quantum dots and heteroatom doped graphene quantum dots using chemical vapor deposition technique. Graphene quantum dots are prepared using alloy-based catalyst and methane as a carbon source. Boron-doped and nitrogen-doped graphene quantum dots are prepared at low temperature using graphite oxide without the use of dialysis bag. Here, the electrochemical lithium and sodium ion storage properties of doped and undoped graphene quantum dots are studied without being used as a supporting material for the performance enhancement as reported in previous reports. Boron doped GQD (B-GQD) exhibits a high specific capacity of 1097 mAh g−1 and 310 mAh g−1 at a specific current of 50 mA g−1 for lithium and sodium ion batteries respectively. B-GQD exhibits high volumetric energy density of 537 Ah L−1 and 214 Ah L−1 with an average voltage of 0.43 V and 0.57 respectively for lithium ion and sodium ion batteries. Also, the cells observe a satisfactory cyclic performance for 500 cycles with good capacity retention. Detailed investigations show that the edge defects present in GQD and doped GQDs help to enhance the electrochemical storage performance of lithium and sodium ions. © 2019 Elsevier B.V.