Here, a novel fabrication method for making free-standing 3D hierarchical porous carbon aerogels from molecularly engineered biomass-derived hydrogels is presented. In situ formed flower-like CaCO₃ molecularly embedded within the hydrogel network regulated the pore structure during in situ mineralization assisted one-step activation graphitization (iMAG), while the intrinsic structural integrity of the carbon aerogels was maintained. The homogenously distributed minerals simultaneously acted as a hard template, activating agent, and graphitization catalyst. The decomposition of the homogenously distributed CaCO₃ during iMAG followed by the etching of residual CaO through a mild acid washing endowed a robust carbon aerogel with high porosity and excellent electrochemical performance. At 0.5 mA cm⁻², the gravimetric capacitance increased from 0.01 F g⁻¹ without mineralization to 322 F g⁻¹ with iMAG, which exceeds values reported for any other free-standing or powder-based biomass-derived carbon electrodes. An outstanding cycling stability of ~104% after 1000 cycles in 1 M HClO₄ was demonstrated. The assembled symmetric supercapacitor device delivered a high specific capacitance of 376 F g⁻¹ and a high energy density of 26 W h kg⁻¹ at a power density of 4000 W kg⁻¹, with excellent cycling performance (98.5% retention after 2000 cycles). In combination with the proposed 3D printed mold-assisted solution casting (3DMASC), iMAG allows for the generation of free-standing carbon aerogel architectures with arbitrary shapes. Furthermore, the novel method introduces flexibility in constructing free-standing carbon aerogels from any ionically cross-linkable biopolymer while maintaining the ability to tailor the design, dimensions, and pore size distribution for specific energy storage applications.