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Defects in liquid crystals serve as templates for nanoparticle (NP) organization; however, NP assembly in cholesteric (Ch) liquid crystals is only beginning to emerge. We show interactive morphogenesis of NP assemblies and a Ch liquid crystalline host formed by cellulose nanocrystals (CNCs), in which both the host and the guest experience marked changes in shape and structure as a function of concentration. At low NP loading, Ch-CNC droplets exhibit flat-ellipsoidal packing of Ch pseudolayers, while the NPs form a toroidal ring- or two cone–shaped assemblies at droplet poles. Increase in NP loading triggers reversible droplet transformation to gain a core-shell morphology with an isotropic core and a Ch shell, with NPs partitioning in the core and in disclinations. We show programmable assembly of droplets carrying magnetic NPs. This work offers a strategy for NP organization in Ch liquid crystals, thus broadening the spectrum of architectures of soft nanostructured materials.