Upconversion nanoparticles (UCNPs) are a class of inorganic fluorophores that follow the anti-Stokes mechanism, to which the wavelength of emission is shorter than absorption. This unique optical behavior generates relatively long-lived intermediate energy levels of lanthanides that stabilize the excitation state in the fluorescence process. Longer-wavelength light sources, e.g., near-infrared (NIR), penetrate deeper into biological materials such as tissue and cells that provide a larger working space for cell biology applications and imaging, whereby UCNPs have recently gained increasing interest in medicine. In this report, the emission intensity of a gadolinium-based UCNP was screened by changing the concentrations of the constituents. The optimized condition was utilized as a luminescent nanoprobe for targeting the mitochondria as a distinguished subcellular organelle within differentiated neuroblastoma cells. The main goal of this study is to illustrate the targeting process within the cells in a native state using modified UCNPs. Confocal microscopy on the cells treated with the functionalized UCNPs indicated a selective accumulation of UCNPs after immunolabeling. To tackle the insolubility of as-synthesized particles in water-based media, the optimized UCNPs were surface-coated with polyamidoamine (PAMAM) dendrimers that due to peripheral amino groups are suitable for functionalizing with peptides and antibodies. Ultimately, we concluded that UCNPs are potentially versatile and ideal tools for NIR bioimaging and capable of making adequate contrast against biomaterials to be detectable in electron microscopy (EM) imaging.