The metal-directed supramolecular synthetic approach has paved the way for the development of functional nanosized molecules. In this work, we report the preparation of the new nanocapsule 3⋅(CF3SO3)8 with a A4B2 tetragonal prismatic geometry, where A corresponds to the dipalladium hexaazamacrocyclic complex Pd-1, and B corresponds to the tetraanionic form of palladium 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin (2). The large void space of the inner cavity and the supramolecular affinity for guest molecules towards porphyrin-based hosts converts this nanoscale molecular 3D structure into a good candidate for host–guest chemistry. The interaction between this nanocage and different guest molecules has been studied by means of NMR, UV/Vis, ESI-MS, and DOSY experiments, from which highly selective molecular recognition has been found for anionic, planar-shaped π guests with association constants (Ka) higher than 109 M−1, in front of non-interacting aromatic neutral or cationic substrates. DFT theoretical calculations provided insights to further understand this strong interaction. Nanocage 3⋅(CF3SO3)8 can not only strongly host one single molecule of M(dithiolene)2 complexes (M=Au, Pt, Pd, and Ni), but also can finely tune their optical and redox properties. The very simple synthesis of both the supramolecular cage and the building blocks represents a step forward for the development of polyfunctional supramolecular nanovessels, which offer multiple applications as sensors or nanoreactors.