Predictive and mechanistically driven access to polynuclear oxo clusters and related materials remains a grand challenge of inorganic chemistry. We here introduce a novel strategy for synthetic control over highly sought-after transition metal {M4O4} cubanes. They attract interest as molecular water oxidation catalysts that combine features of both heterogeneous oxide catalysts and nature's cuboidal {CaMn4O5} center of photosystem II. For the first time, we demonstrate the outstanding structure-directing effect of straightforward inorganic counteranions in solution on the self-assembly of oxo clusters. We introduce a selective counteranion toolbox for the controlled assembly of di(2-pyridyl) ketone (dpk) with M(OAc)2 (M = Co, Ni) precursors into different cubane types. Perchlorate anions provide selective access to type 2 cubanes with the characteristic {H2O-M2(OR)2-OH2} edge-site, such as [Co4(dpy-C{OH}O)4(OAc)2(H2O)2](ClO4)2. Type 1 cubanes with separated polar faces [Co4(dpy-C{OH}O)4(L2)4] n+ (L2 = OAc, Cl, or OAc and H2O) can be tuned with a wide range of other counteranions. The combination of these counteranion sets with Ni(OAc)2 as precursor selectively produces type 2 Co/Ni-mixed or {Ni4O4} cubanes. Systematic mechanistic experiments in combination with computational studies provide strong evidence for type 2 cubane formation through reaction of the key dimeric building block [M2(dpy-C{OH}O)2(H2O)4]2+ with monomers, such as [Co(dpy-C{OH}O)(OAc)(H2O)3]. Furthermore, both experiments and DFT calculations support an energetically favorable type 1 cubane formation pathway via direct head-to-head combination of two [Co2(dpy-C{OH}O)2(OAc)2(H2O)2] dimers. Finally, the visible-light-driven water oxidation activity of type 1 and 2 cubanes with tuned ligand environments was assessed. We pave the way to efficient design concepts in coordination chemistry through ionic control over cluster assembly pathways. Our comprehensive strategy demonstrates how retrosynthetic analyses can be implemented with readily available assembly directing counteranions to provide rapid access to tuned molecular materials.