Clustering chemistry is a key point in the design of the secondary building units (SBUs) that comprise metal-organic frameworks (MOFs). In this work, zirconium-carboxylate clustering processes in alcohol/water mixtures are studied using the monocarboxylic benzoic and hydroxybenzoic acids to avoid the polymerization. Mass-spectroscopy measurements revealed the presence of hexa- and pentanuclear species and evidenced the acid-base nature and pH dependence of the transformation between both species. The X-ray diffraction analysis of six new compounds showed that they are closely related to the [Zr6(O)4(OH)4(OOC)12] SBU found in many MOFs by removing carboxylic ligands in the case of the [Zr6(μ3-O)4(μ3-OH)4(μ-OOCR)8(H2O)8]4+ species or by additionally removing one of the metal centers for the [Zr5(μ3-O)2(μ3-OH)6(μ-OOCR)4(H2O)11(alcohol)]6+ entities. The unsaturated hexameric clusters exhibit different dispositions of their eight carboxylate ligands in such a way that the remaining four carboxylate-free positions are arranged according to a square planar or tetrahedral symmetry. The pentameric cluster implies an unprecedented core nuclearity in discrete zirconium species and thus its isolation provides a novel building block for the design of metal-organic materials. Last, but not least, it is claimed that these highly positively charged polynuclear clusters are potential building block to prepare a plethora of ionic compounds by combining them with different counterions, providing some successful examples.