The central aim of this PhD thesis is to develop synthetic procedures to construct metal organic-frameworks (MOFs) able to host/build up molecular-based species, such as metal ions with particular coordination environments, single atom catalysts (SACs), sub-nanometric metal clusters (SNMCs) and supramolecular coordination complexes (SCCs), otherwise hardly accessible, with high catalytic reactivity and in a multigram scale. The nature of the final assemblies has been characterised with a myriad of physical techniques, where taking advantage of the high crystallinity and structural robustness of the MOFs used as platforms, single-crsytal X-ray crystallography play a promienet role and provide us with unique snapshots of the novel hybrid materials assembled. Here, it is worth to remark that the obtention, stabilization and characterization of such unique hybrid species is an extraordinary challenge. Thus, this in itself reflect the success of the results presented in this PhD thesis. In order to do so, in this PhD thesis we have worked with oxamate- and oxamidate-based MOFs, derived from robust aromatic diamines and aminoacids, respectively, constructed by applying the rational metalloligand strategy. This strategy consist on the use of dinuclear copper(II) building blocks that act as metalloligands toward transition or alkaline-earth metal ions to assembly the target framework. Then, we have taken advantage of the outstanding crystallinity and structural robustness of these MOFs to use them as chemical nanoreactors by means of different post-synthetic methodologies (PSMs), which enable us to encapsulate and/or in-situ construct within their channels unique molecular-based catalyst. Besides a general introduction to put in context the results obtained during this PhD thesis, we have structured them in three different chapters. The first one is focused on the application of post-synthetic partial cation exchange to obtain a material with up to three different metal ions (Cu, Ni and Pd) with potential catalytic activity to explore their use in tandem/cascade catalytic reactions. In the third chapter we move to the obtention of SACs and SNMCs. In particular, we present isolated Ag(0)2 SNMCs and Pd(0) SACs, as well as the combination of SACs and SNMCs with Ag(0)2 Fe(3+). Then, in the fourth chapter, we exploit the rich host-guest chemistry of the selected MOF to build SCCs, where the intrinsic catalytic properties of pivotal palladium atoms can be fully exploited. Finally, we have included a general conclusions section together with future perspectives on the basis of the research work developed in this PhD thesis.