The formation of stable and ordered free-standing porous supramolecular assemblies of nanoparticles with sizes and geometries controlled at different length scales is demonstrated by a double-templating strategy. Our technique combines the directed assembly of particles, templating using nanoimprint lithography (NIL), and supramolecular layer-by-layer (LbL) assembly. First, 500-nm β-cyclodextrin (CD)-functionalized polystyrene (PS) particles were assembled by convective assembly onto a sacrificial polymer template patterned with a predefined geometry and size using NIL, forming a 3D crystal architecture of particles. LbL assembly of alternating supramolecular host- and guest-functionalized glues of CD-functionalized Au (Au-CD) nanoparticles and adamantyl (Ad) dendrimers, sized between 3–5 nm, within the preformed PS-particle crystal effectively bound the particles together into a particle composite. These particle composites were released from the substrate together with the polymer template, and transferred onto a target substrate. The particle crystal integrity, order and functionality were preserved. Rinsing the structure with dichloromethane removed the PS core material together with the polymer template, resulting in interconnected porous capsules, the sizes and shapes of which are fully determined by the PS core size and the polymer template definition. Again, integrity and shape were preserved in the rinsing step. These capsules were capable of storing organic fluorescent molecules using specific interactions.