Multicopper active sites for small molecule activation in materials and enzymatic systems rely on controlled but adaptable coordination spheres about copper clusters for enabling challenging chemical transformations. To translate this constrained flexibility into molecular multicopper complexes, developments are needed in both ligand design for clusters and synthetic strategies for modifying the cluster cores. The present study investigates the chemistry of a class of pyridyldiimine-derived macrocycles with geometrically flexible aliphatic linkers of varying lengths (nPDI2, n = 2, 3). A series of dicopper complexes bound by the nPDI2 ligands are described and found to exhibit improved solubility over their parent analogs due to the incorporation of 4-tBu groups on the pyridyl units and the use of triflate counterions. The ensuing synthetic study investigated methods for introducing various bridging ligands (µ-X; X = F, Cl, Br, N3, NO2, OSiMe3, OH, OTf) between the two copper centers within the macrocycle-supported complexes. Traditional anion metathesis routes were unsuccessful, but the abstraction of bridging halides resulted in “open-core” complexes suitable for capturing various anions. The geometric flexibility of the nPDI2 macrocycles was reflected in the various solid-state geometries, Cu–Cu distances, and relative Cu coordination spheres on variation in the identity of the captured anion.