Fluorescent nanoparticles and nanocapsules (FNPs) were synthesized via a one-pot RAFT miniemulsion process copolymerizing BODIPY-methacrylate and styrene in water. Ultra-bright sub-100 nm core–shell nanoparticles could be obtained with BODIPY covalently linked in the core, and possessing various shells. The nature and architecture of the particle shells could be tuned by using different macromolecular RAFT (macro-RAFT) agents in the miniemulsion polymerization process. The macro-RAFT agents were composed of poly(ethylene oxide) acrylate (PEOA) and/or acrylic acid (AA), owing to their biocompatibility and functionality respectively, in different proportions. Interestingly, with comb-like macro-RAFT agents comprising a high number of PEOA, nanocapsules were formed, while with linear macro-RAFT agents or with those exhibiting a high number of AA, full core–shell nanoparticles were obtained. For all the structures the control over the polymerization, the size, morphology, and zeta-potential as well as the photophysical properties were measured and compared with FNPs exhibiting a linear PEO-b-PAA block copolymer shell structure (C. Grazon, J. Rieger, R. Méallet-Renault, G. Clavier and B. Charleux, Macromol. Rapid Commun., 2011, 32, 699). Regardless of the shell structures, the brightness of the formed nanoparticles was estimated to be 100–1000 times higher than that of quantum dots. Ultimately, the shell of the different FNPs was functionalized with a second fluorophore via the AA's carboxyl groups. Thus, water-soluble ultra-bright FNPs with two fluorophores in distinct environments (water and in polystyrene) were obtained. They should have great potential for bioimaging applications.