This article presents a new distributed and reconfigurable strategy for global economical consensus operation of multiple, interconnected dc microgrid clusters in a leader–follower graph architecture. The generation costs associated with the distributed energy resources are optimized globally by observer-based controllers in a multilayered hierarchical control structure, equipped with privacy-preserving feature. Self-rearranging and event-based reconfiguration of graphs are also incorporated for obtaining feasible solution to the economic dispatch problem. This is an important aspect of the proposed work as, unlike previously reported research works, it equally prioritizes both voltage regulation and optimal operation. Moreover, continuity of supply to critical loads is a challenging criterion in autonomous systems in which the pinning or leader node plays a pivotal role. Therefore, the multifold benefits of choosing the highest generation unit as the leader in improving the power quality is highlighted for the first time, which remained undiscovered in previous works in literature. The feasibility of the proposed scheme is tested by time-domain simulations in MATLAB/Simulink. Moreover, the results obtained from the controller hardware in loop environment using a real-time digital simulator and field-programmable-gate-array-based WAVECT controller demonstrate the economical operation of the clusters with renewable energy sources.