We report a small-angle neutron scattering (SANS) study of the influence of compositional separation (CS) on the magnetic microstructure of sputtered Co-22at% Cr thin films deposited at substrate temperatures (T S ) of 40-400°C. Using vibrating sample magnetometry and nuclear magnetic resonance, we observed that CS producing a Co-enriched component develops as T S increases and becomes most prominent at around 250°C with a maximum saturation magnetization. At T S over 400°C compositional homogenization occurs. The SANS spectra show that all the films exhibit much larger scattering cross-sections than that of a compositionally homogeneous Co-22at% Cr bulk alloy sample. This indicates that CS promotes both magnetic and chemical microstructures in the thin films. The SANS spectra are observed to change systematically with the variation in T S . An analysis of these spectra suggests that CS produces in-grain columnar magnetic microstructures with small sizes of several nanometers at T S of 40-200°C, and these microstructures become particulate at T S of 300 and 400°C, where compositional homogenization occurs. It is shown that T S is a critical factor in the formation of the magnetic microstructures.