We investigate the bulk and surface features of the crystalline–amorphous transitions in binary Al–Mo alloy thin films as a function of Mo composition using transmission electron microscopy, X-ray diffraction and atomic force microscopy analysis, as well as thermodynamic modeling. Of the alloys tested, the minimum in the root mean square (rms) surface roughness and correlation length occurs at the Al–32 at.% Mo composition, which corresponds to the maximum volume fraction of the amorphous phase and the minimum volume fraction of the body centered cubic nanocrystallites. The rms surface roughness of the 32 at.% Mo films is on the order of a single nanometer, compared with nearly 80 nm for the 50 at.% Mo film. A structure–zone map is constructed to relate the surface morphology of the films to their bulk microstructure. A thermodynamic model developed by Miedema and coworkers was used to predict the general trends observed in the microstructural evolution as a function of film composition.