The anisotropic flexible metamaterial absorber (FMA) structure comprises a resonating layer, a ferrite-based flexible substrate layer, and a back layer. The sol-gel method is used to prepare the ferrite-based nanomaterial for enhancing absorbability. The solution prepared material is according to the formula of MgxCo(0.90−x)Zn0.10Fe2O4 and specified as X25, X50, X75 for X = 25%, 50%, and 75%, respectively. Then the proposed ferrites materials are characterized by XRD, and FESEM, respectively. Moreover, the magnetic and dielectric properties of the proposed MgxCo(0.90−x)Zn0.10Fe2O4 ferrites samples were explored for microwave applications. The dielectric constants and loss tangents of the fabricated, flexible substrates are measured at a frequency range of 3–7 GHz using the DAK 3.5. The computed relative permittivity values are 2.95 for X25, 3.55 for X50, and 4.05 for X75, respectively, while the loss tangents values are 0.00295 for X25, 0.00495 for X50, and 0.00695 for X75. Whereas the permeability and magnetic loss tangent values varied from 0.875 to 1.00 and 0.00225–0.00585, respectively. Finally, the resonators of the absorber consist of a Y-style shape, square-shaped metallic plate resonator, square ring resonator (SRR), and cross-liked shape. The proposed flexible metamaterial absorber (FMA) structure is developed on MgxCo(0.90−x)Zn0.10Fe2O4 nanomaterial-based flexible substrate with dimensions of 0.110λ x 0.110λ x 0.017λ to validate the design experimentally. The electrical dimension is calculated at a 5.5 GHz resonance frequency. The simulated results from the CST Microwave Studio simulator reveal that absorption peaks at 5.5 GHz with a 99.99% absorption that includes the C band frequency that can be used in satellite applications. The proposed FMA structure achieved a 60° incident angle response for TE and TM modes. The structure has superiority with compact dimensions, lightweight, and flexibility and can be used for C band wireless communications.