We present a systematic analysis of the atomic-scale imaging capabilities for mineral surfaces in a liquid environment in single and dual mode amplitude modulation dynamic force microscopy. To study the difference in sensitivity between the first and second eigenmode phase signals we investigate the observed atomic-scale contrasts of the mica–water interface under varying imaging conditions. For this purpose, we systematically change the main imaging parameters including the setpoint amplitude of the imaging feedback, the free oscillation amplitudes of the first and second flexural eigenmodes, and their ratio. This allows for an in-depth analysis of the sensitivities of the first and second eigenmode phase signals to draw conclusions regarding the underlying physical mechanisms and the interpretation of the contrast in the multi-frequency technique.