the importance of surface preparation and the effect of surface oxides, the complex effect of superconductor film structure on microwave losses is not yet fully understood. In this study, we investigate the microwave properties of niobium resonators with different crystalline properties and related surface topographies. We analyze a series of magnetron sputtered films in which the Nb crystal orientation and surface topography are changed by varying the substrate temperatures between room temperature and 975 K. The lowest-loss resonators that we measure have quality factors of over one million at single-photon powers, among the best ever recorded using the Nb on sapphire platform. We observe the highest quality factors in films grown at an intermediate temperature regime of the growth series (550 K) where the films display both preferential ordering of the crystal domains and low surface roughness. Furthermore, we analyze the temperature-dependent behavior of our resonators to learn about how the quasiparticle density in the Nb film is affected by the niobium crystal structure and the presence of grain boundaries. Our results stress the connection between the crystal structure of superconducting films and the loss mechanisms suffered by the resonators and demonstrate that even a moderate change in temperature during thin film deposition can significantly affect the resulting quality factors.