Wastewater contaminated with antibiotics is a major environmental challenge. The oxidation process is one of the most common and effective ways to remove these pollutants. The use of metal-free, green, and inexpensive catalysts can be a good alternative to metal-containing photocatalysts in environmental applications. We developed here the green synthesis of bio-graphenes by using natural precursors (Xanthan, Chitosan, Boswellia, Tragacanth). The use of these precursors can act as templates to create 3D doped graphene structures with special morphology. Also, this method is a simple method for in situ synthesis of doped graphenes. The elements present in the natural biopolymers (N) and other elements in the natural composition (P, S) are easily placed in the graphene structure and improve the catalytic activity due to the structural defects, surface charges, increased electron transfers, and high absorption. The results have shown that the hollow cubic Chitosan-derived graphene has shown the best performance due to the doping of N, S, and P. The Boswellia-derived graphene shows the highest surface area but a lower catalytic performance, which indicates the more effective role of doping in the catalytic activity. In this mechanism, O2 dissolved in water absorbs onto the positively charged C adjacent to N dopants to create oxygenated radicals, which enables the degradation of antibiotic molecules. Light irradiation increases the amount of radicals and rate of antibiotic removal.