The sources of phase angle contrast in measurements using atomic force microscopy and the effect of free amplitude and setpoint on phase angle contrast images of several nanocomposites and molecularly thick lubricant films have been studied. Phase angle contrast depends on viscoelastic properties and interfacial adhesion, as well as on the selection of free amplitude and setpoint. Phase angle contrast is a stronger function of viscoelastic properties with increasing free amplitude or setpoint. However, the effect of adhesion on phase angle contrast becomes more dominant at low free amplitudes or setpoints. As a result of competition between viscoelasticity and adhesion, the phase angle contrast may flip with changes in free amplitude and setpoint. A comparison between topographic, friction and phase angle images shows that phase angle images give information that cannot be obtained from topographic or friction images. By optimizing free amplitude and setpoint, the phase angle contrast imaging technique can be used to detect changes in composition across polymer nanocomposites and molecularly thick lubricated surfaces.