Inspired by the reported crystal structure of compound 1, we aimed to synthesize and determine the structure of compound 2, where two imidazolium (H2im+) ions serve as diamagnetic countercations. Here, we report the thermal stabilities, FT–IR, visible, and RSE spectra, as well as the magnetic properties of both compounds. In these structures, µ-EDTA acts as a pentadentate chelator for both terminal Cu centers within the centrosymmetric linear trinuclear anion. The Cu(µ-EDTA) chelates bind to the central Cu(Him)4 unit in subtly different ways: in compound 1, µ-EDTA has a free acetate arm and binds the central Cu(II) center through a syn,anti-carboxylate group. In contrast, in compound 2, the non-chelating acetate arm serves as a monodentate O-donor to the central Cu(II) atom, increasing the Cu(terminal)···Cu(central) distance from 6.08 Å in 1 to 6.80 Å in 2. Additionally, pairs of H2im+ ions in compound 2 display antiparallel π-stacking interactions. We conclude that the H2im+ counterions in compound 2 enable the magnetic isolation of the nearly identical trinuclear anion present in both compounds. DFT calculations further support the role of different interactions in stabilizing each crystal structure. In compound 2, dominant contributions from N–H···O hydrogen bonds and π-stacking interactions are accompanied by other, less conventional interactions, such as multiple C–H···O contacts and an O···CO(π-hole) interaction within the trinuclear anion.