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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 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 1M 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 design, dimensions and pore size distribution for specific energy storage applications.