We report on the interplay of magnetic properties and intrinsic strain in ferromagnetic nickel nanocubes with cubic anisotropy. Via coherent x-ray diffraction imaging we observed compressive stress at the bottom surface of these cubes. The nanocubes with {100} facets described and imaged in this study were synthesized using a single-step CVD process. Micromagnetic simulations predict the presence of vortices at remanence in the absence of strain. The effects of strain resulting from the compressive stress on the magnetic response of the ferromagnetic cubes is investigated. We observe that measured intrinsic strain is too low to change the magnetic anisotropy of ferromagnetic cubes but topological behavior of magnetic vortices is sensitive to even this low range of strain.