The controllable design of functional nanostructures for energy and environmental applications represents a critical yet challenging technology. The existing fabrication strategies focus mainly on increasing the number of accessible active sites. However, these techniques generally necessitate complex chemical agents and suffer from limited experimental conditions delivering high costs, low yields, and poor reproducibility. The present work reports a new strategy for controllable synthesis of a hybrid system including mixed iron oxide nanostructures enriched with non-stoichiometric Fe_21.34O₃₂ and Fe³⁺[Fe_5/3³⁺□_1/3²⁺]O₄ phases, which possess a high concentration of oxygen and Fe²⁺ vacancies, and a mesoporous carbon-based scaffold (MCS), which was dervied from coffee residues, with graphitic surface and perforated architecture. The nanoperforates acted as trapping sites to localise the Fe_xO_y nanoparticles, thereby boosting the density of accessible active sites. Additionally, at the interfacial regions between the Fe_xO_y crystallites, a high density of oxygen vacancies with an oriented pattern was shown to create superlattice structures. The energy storage functionality of the defect-rich MCS/Fe_xO_y nanostructure with nanoperforated architecture was investigated, where the results exhibited a high gravimetric capacitance of 540 F g⁻¹ at a current density of 1 A g⁻¹ with outstanding capacitance retention of 73.6% after 14 000 cycles.