Upconversion nanoparticles are a promising class of materials for bioimaging. Their attractive optical properties are influenced by their crystalline phase, size, and morphology resulting from the preparation method employed. Herein, we synthesized NaYF4:Yb,Er nanocrystals by the co-precipitation method followed by a heat treatment step. The influence of the treatment temperature and the type of reactor on the phase transition from the α-cubic to the β-hexagonal phase was investigated. We found that before the phase transition, the size and shape of α-NaYF4:Yb,Er nanocrystals evolved due to a coalescence mechanism with microtubular reactors. In contrast to the flask system, we also observed an anisotropic growth of β-NaYF4:Yb,Er nanorods in microtubes whose length can be controlled by adjusting the temperature. The diameter of microtubes plays a critical role in the shape evolution of the final products from spheres to nanorods. The type of reactor and thus the resulting temperature gradient could be considered as a promising parameter to control the phase, shape and size of UCNPs without changing the chemical composition.