Lacunary polyoxometalates (LPOMs) are key precursors for the synthesis of functional POMs. To date, reviews dedicated to behavioral studies of LPOMs often comprise the role of metal ions, including transition metal (TM) and rare earth (RE) ions, in extending and stability of high-nuclearity clusters. In contrast, the role of organic ligands in the structures and properties of lacunary-based hybrids has remained less explored. In this review, we focus on the role of organic fragments in the self-assembling process of POM-based architectures and discuss relationships between the nature and structure of organic ligand and properties such as the topology of hybrid inorganic–organic material in RE and TM-RE heterometallic derivatives of lacunary Keggin-type POMs. The effects of organic fragment in mixed ligand hybrids are also briefly reviewed.