We investigate by a scanning probe technique termed phase-electrostatic force microscopy the local electrostatic potential and its correlation to the morphology of the organic semiconductor layer in operating ultra-thin film pentacene field effect transistors. This technique yields a lateral resolution of about 60 nm, allowing us to visualize that the voltage drop across the transistor channel is step-wise. Spatially localized voltage drops, adding up to about 75% of the potential difference between source and drain, are clearly correlated to the morphological domain boundaries in the pentacene film. This strongly supports and gives a direct evidence that in pentacene ultra-thin film transistors charge transport inside the channel is ultimately governed by domain boundaries.