The self‐assembly of porous molecular nanocapsules offer unique opportunities to investigate a range of interesting phenomena and applications. However, to design nanocapsules with pre‐defined properties, thorough understanding of their structure‐property relation is required. Here, we report the self‐assembly of two elusive members of the Keplerate family, [Mo132Se60O312(H2O)72(AcO)30]42− {Mo132Se60} 1 and [W72Mo60Se60O312(H2O)72(AcO)30]42− {W72Mo60Se60} 2, that have been synthesised using pentagonal and dimeric ([Mo2O2Se2]2+) building blocks and their structures have been confirmed via single crystal X‐ray diffractions. Our comparative study involving the uptake of organic ions and the related ligand exchange of various ligand sizes by the {Mo132Se60} and previously reported Keplerates {Mo132O60}, {Mo132S60} based on the ligand exchange rates, revealed the emergence of increased “breathability” that dominates over the pore size as we transition from the {Mo132S60} to the “softer” {Mo132Se60} molecular nano‐container.