Quantum key distribution (QKD) has often been hailed as a reliable technology for secure communication in cyber-physical microgrids. Even though unauthorized key measurements are not possible in QKD, attempts to read them can disturb quantum states leading to mutations in the transmitted value. Further, inaccurate quantum keys can lead to erroneous decryption producing garbage values, destabilizing microgrid operation. QKD can also be vulnerable to node-level manipulations incorporating attack values into measurements before they are encrypted at the communication layer. To address these issues, this paper proposes a secure QKD protocol that can identify errors in keys and/or nodal measurements by observing violations in control dynamics. Additionally, the protocol uses a dynamic adjacency matrix-based formulation strategy enabling the affected nodes to reconstruct a trustworthy signal and replace it with the attacked signal in a multi-hop manner. This enables microgrids to perform nominal operations in the presence of adversaries who try to eavesdrop on the system causing an increase in the quantum bit error rate (QBER). We provide several case studies to showcase the robustness of the proposed strategy against eavesdroppers and node manipulations. The results demonstrate that it can resist unwanted observation and attack vectors that manipulate signals before encryption.