This research delves into the influence of intrinsic decoherence on the behavior of quantum correlations and coherence between two interacting qubits in a graphene-based system. To evaluate the amount of nonclassical correlations in the system, we employ local quantum uncertainty (LQU), and to assess quantum coherence we use the relative entropy of coherence (Cr) and l1-norm (Cl1). We assume that the system is initially prepared in an extended-Werner-like (EWL) state, and we investigate how these quantifiers evolve over time and examine their sensitivity to various graphene layer system parameters, mixture parameter of the initial state and the intrinsic decoherence rate. Our results indicate that by adjusting the wave number operators, decreasing the intrinsic decoherence rate, and increasing the initial state mixing parameter, it is possible to enhance both quantum correlations and coherence within the two-dimensional honeycomb lattice system. In addition, we found that quantum coherence is more resilient to intrinsic decoherence than LQU, moreover, the l1-norm is more robust than the relative entropy of coherence.