In this paper, we examine the impact of three-dimensional grating layers embedded at selected locations in an organic solar cell structure to obtain enhanced efficiency. The design, simulations, and optimizations were carried out using an in-house tool based on the rigorous coupled-wave analysis (RCWA) method developed on the MATLAB R2019a platform. An optimal organic solar cell structure design with a top grating layer exhibited an increase of 7.47% in the short-circuit current density compared to an organic solar cell structure with a smooth top layer. The power conversion efficiency (PCE) increase was mainly due to increased light confinement in the thin absorbing layer. Adding an embedded grating layer in the absorption layer resulted in a significant increase in the absorptance spectral bandwidth, where the short-circuit current density increased by 10.88%. In addition, the grating cells yielded a substantial improvement in the cell’s conical absorptance since the existence of a surface plasmon polariton (SPP) in the back metal gratings increases the confinement properties. Further, the effect of a pyramid-shaped embedded grating array was a slight improvement in the PCE compared to the rectangular-shaped grating arrays. We showed that a pyramid-grating can act as a nano black-body layer, increasing the absorption for a wide range of azimuthal and polar incident angles.