In the past few years, defect‐engineered metal–organic frameworks (DEMOFs) have been studied due to the plethora of textural, catalytic, or magnetic properties that can be enhanced by carefully introducing defect sites into the crystal lattices of MOFs. In this work, the spatial distribution of two different non‐defective and defective linkers, namely 1,3,5‐benzenetricarboxylate (BTC) and 5‐cyano‐1,3‐benzenedicarboxylate (CYDC), respectively, has been studied in different DEMOF crystals of the HKUST‐1 topology. Raman micro‐spectroscopy revealed a nonhomogeneous distribution of defect sites within the [Cu3(btc)2−x(cydc)x] crystals, with the CYDC linker incorporated into defect‐rich or defect‐free areas of selected crystals. Additionally, advanced bulk techniques have shed light on the nature of the copper species, which is highly dynamic and directly affects the reactivity of the copper sites, as shown by probe molecule FTIR spectroscopy. Furthermore, electron microscopy revealed the effect of co‐crystallizing CYDC and BTC on the crystal size and the formation of mesopores, further corroborated by X‐ray scattering analysis. In this way we have demonstrated the necessity of utilizing micro‐spectroscopy along with a whole array of bulk spectroscopic techniques to fully describe multicomponent metal–organic frameworks.