The Pauli exclusion principle (PEP), a cornerstone of quantum mechanics and whole science, states that in a system, two fermions can not simultaneously occupy the same quantum state. Several experimental tests have been performed to place increasingly stringent bounds on the validity of PEP. Among these, the series of VIP experiments, performed at the Gran Sasso Underground National Laboratory of INFN, is searching for PEP-violating atomic X-ray transitions in copper. In this paper, the upgraded VIP-3 setup is described, designed to extend these investigations to higher-Z elements such as zirconium, silver, palladium, and tin. We detail the enhanced design of this setup, including the implementation of cutting-edge, 1 mm thick, silicon drift detectors, which significantly improve the measurement sensitivity at higher energies. Additionally, we present calculations of expected PEP-violating energy shifts in the characteristic lines of these elements, performed using the multi-configurational Dirac–Fock method from first principles. The VIP-3 realization will contribute to ongoing research into PEP violation for different elements, offering new insights and directions for future studies.