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Purpose The purpose of this paper is to present the implementation of a balanced domain decomposition approach for the numerical simulation of large electro-quasistatic (EQS) systems in biology. The numerical scheme is analyzed and first applications are discussed. Design/methodology/approach The scheme is based on a finite element discretization of the individual domains obtained by decomposition and a physically consistent inter-domain coupling realized via Robin boundary conditions. The proposed algorithms can efficiently be implemented on a highly parallelized computing grid. Findings The feasibility and applicability of the method is proven. Further, a couple of technical details are found that increase the efficiency of the method. Originality/value The presented method offers an enhanced geometrical flexibility and extensibility to simulate larger cell systems with higher model resolution compared to other methods presented in the literature. The presented analysis provides an understanding of the balanced coupling scheme for large EQS systems.