N-polar InAlN thin films were grown by plasma-assisted molecular beam epitaxy on freestanding GaN substrates under N-rich conditions. Indium and aluminum fluxes were varied independently at substrate temperatures below and above the onset of thermal desorption of indium. At low temperatures, the InAlN composition and growth rate are determined by the group-III fluxes. With increasing substrate temperature, the surface morphology transitions from quasi-3D to a smooth, 2D morphology at temperatures significantly above the onset of indium loss. At higher temperatures, we observe increased indium evaporation with higher indium fluxes and a suppression of indium evaporation with increased aluminum flux. The final optimized InAlN thin film results in step-flow morphology with rms roughness of 0.19 nm and high interfacial quality.