Magnesium oxide films prepared as monolayer, amorphous, and epitaxial films have different properties such as semiconducting, ferromagnetic, and dielectric behavior, respectively. Understanding the variation in these properties requires detailed information about the atomic structure of the different MgO films. In the present study, one important synthesis method, ballistic deposition, is studied, and the influence of the deposition temperature on the resulting atomic structure of the films is analyzed in detail, employing XRD, SEM, EDX, XPS, and Raman scattering. At −190 °C, compact, light-yellow films are obtained, which consist of small crystallites adopting the rock salt structure with an excess of oxygen at the grain boundaries. However, at 25 °C, nearly stoichiometric, white, columnar films exhibiting a superfilled rock salt structure are grown. In the first case, dioxygen species are formed by connecting the oxygen shells of adjacent small crystalline grains, and in the second case such species appear due to the partial occupation of tetrahedral sites in the rock salt structure. These observations should open new prospects of fine-tuning the properties of MgO films and enhance the performance of devices employing such films.