Lanthanide-doped upconversion nanoparticles (UCNPs) are of great interest for biomedical applications. Currently, the applicability of UCNP bionanotechnology is hampered by the generally low luminescence intensity of UCNPs and inefficient energy transfer from UCNPs to surface-bound chromophores used e.g. for photodynamic therapy or analyte sensing. In this work, we address the low-efficiency issue by developing versatile core-shell nanostructures, where high-concentration sensitizers and activators are confined in the core and shell region of representative hexagonal NaYF4:Yb,Er UCNPs. After doping concentration optimization, the sensitizer-rich core is able to harvest/accumulate more excitation energy and generate almost one order of magnitude higher luminescence intensity than conventional homogeneously doped nanostructures. At the same time, the activator ions located in the shell enable a ∼6 times more efficient resonant energy transfer from UCNPs to surface-bound acceptor dye molecules due to the short distance between donor-acceptor pairs. Our work provides new insights into the rational design of UCNPs and will greatly increase the general applicability of upconversion nanotechnologies.