Spatial distribution of highly energetic negative ions inherent in magnetron sputtering of oxides has long made low temperature deposition unsuitable for high quality films uniform over relatively large areas. Here we examine the distributions of structure as well as physical properties of magnetron sputtered Al-doped ZnO (AZO) films deposited at low temperatures (< 393 K) in which the bombardment from the negative oxygen ions was systematically studied by changing the discharge voltage (i.e., ion energy) and the substrate position (i.e., ion flux). The film structure was characterized by X-ray diffraction, Raman spectroscopy, and transmission electron microscopy; and the electrical and optical properties were obtained by a Hall system and Spectroscopic Ellipsometry. We found (i) that uniform yet high crystallite quality films can be obtained only when the energy of the negative ions was set below a threshold; (ii) that the ion flux exerted an ever-decreasing effect on modifying the film structure as the ion energy was reduced; and (iii) that a set of structural criteria, incorporating crystallite quality (orientations, size, lattice spacing) and point defects, were derived for low resistivity AZO films. The benefit of lowering the ion energy is then explained in terms of the favorable competition between radiation-induced defect generation and the subsequent dynamic annealing. These findings may pave a way for large-area coating of high quality AZO films at low temperatures.