The photoisomerization of a new 4,4’‐diamidoazobenzene model is investigated with ion mobility‐mass spectrometry. Taking observations of previous studies and new control experiments into consideration, a mechanism for a fast thermal (Z)→(E)‐isomerization of azobenzenes during ionization is proposed. The experiments clearly show that a fast (Z)→(E) isomerization is operative when the azo group is protonated, while it can be prevented, when another protonation site remote from the azo group is offered. Besides this, the peak integration ratio in the ion mobilogram is shown to closely correlate with the photoisomer ratio in solution. Future prospects for applications in photocatalysis and systems chemistry are discussed.