In this study, a novel nanohybrid composite was fabricated via the incorporation of manganese ferrite (MnFe2O4) nanoparticles into the integrated surface of reduced graphene oxide (rGO) and black cumin seeds (BC). The nanohybrid composite was prepared by a simple co-precipitation method and characterized by several spectroscopic and microscopic techniques. The characterization analysis revealed that the rGO-BC surface was decorated with the MnFe2O4. The strong chemical interaction (via electrostatic and H-bonding) between the integrated surface of rGO-BC and MnFe2O4nanoparticles has been reported. The prepared composite was highly porous with a heterogeneous surface. The average size of the prepared composite was reported in the ranges of 2.6–7.0 nm. The specific surface area of the prepared composite was calculated to be 50.3 m2/g with a pore volume of 0.061 cc/g and a half pore width of 8.4 Å. As well, many functional sites on the nanohybrid composite surface were also found. This results in the excellent adsorption properties of nanohybrid composite and the effectual elimination of methylene blue dye from water. The nanohybrid was tested for various linear isotherms, such as Langmuir and Freundlich, for the adsorption of methylene blue dye. The Freundlich isotherm was the well-fitted model, proving the adsorption is multilayer. The maximum Langmuir adsorption capacity of nanohybrid composite for methylene blue was reported to be 74.627 mg/g at 27 °C. The adsorption kinetics followed the pseudo-second-order recommended surface interaction between the dye and nanohybrid composite. The interaction between methylene blue and the nanohybrid composite was also confirmed from the FTIR spectrum of the methylene blue-loaded adsorbent. The rate-determining step for the present study was intraparticle diffusion. Temperature-dependent studies of methylene blue adsorption were also carried out to estimate adsorption’s free energy, enthalpy, and entropy. The methylene blue adsorption was feasible, spontaneous, and endothermic. A comparison study revealed that the present materials could be successfully prepared and used for wastewater treatment.