We have studied the effects of low-temperature sputter preparation and subsequent heat treatment of Co79Cr21 thin films with emphasis on their microstructure and magnetic properties. Preparation at −196 °C resulted in textured films which did not show the presence of magnetic Co-rich regions. The saturation magnetization moment, Ms, of these films was similar to their homogeneous alloy phase. Conventionally sputtered films (substrate temperature>room temperature) had higher values of Ms than films prepared at −196 °C. A 1-h heat treatment at 500 °C in vacuum reduced the Ms of both films. The results suggest rearrangement of atoms through thermal diffusion. For the films sputtered at −196 °C (liquid-nitrogen temperature) an atomistically ordered phase can be proposed based on hexagonal Co which minimizes the presence of nearest Cr-Cr neighbors. This maximizes the moment quenching activity of Cr on Co and reduces the saturation moment over the one of a fully random material for segregated films prepared at higher temperature reductions in Ms can also be due to dilution of Co concentration in Co-rich regions.