Metal–organic frameworks (MOFs) with the Zr6O4(OH)4 secondary building unit (SBU) have been of particular interest for potential commercial and industrial uses because they can be easily tailored and are reported to be chemically and thermally stable. However, we show that there are significant changes in chemical and thermal stability of Zr6O4(OH)4 MOFs with the incorporation of different organic linkers. As the number of aromatic rings is increased from one to two in 1,4-benzene dicarboxylate (UiO-66, ZrMOF–BDC) and 4,4′-biphenyl dicarboxylate (UiO-67, ZrMOF–BPDC), the Zr6O4(OH)4 SBU becomes more susceptible to chemical degradation by water and hydrochloric acid. Furthermore, as the linker is replaced with 2,2′-bipyridine-5,5′-dicarboxylate (ZrMOF–BIPY) the chemical stability decreases further as the MOF is susceptible to chemical breakdown by protic chemicals such as methanol and isopropanol. The results reported here bring into question the superior structural stability of the UiO-67 analogs as reported by others. Furthermore, the degradation mechanisms proposed here may be applied to other classes of MOFs containing aromatic dicarboxylate organic linkers, in order to predict their structural stability upon exposure to solvents.