The origin of a large negative threshold voltage observed in monolayer (ML) field effect transistors (FETs) is explored using in-situ electrical measurements through confining the thickness of an active layer to the accumulation layer thickness. Using ML pentacene FETs combined with gated multiple-terminal devices and atomic force microscopy, the effect of electronic and structural evolution of a ML pentacene film on the threshold voltage in an FET, proportional to the density of deep traps, was probed, revealing that a large negative threshold voltage found in ML FETs results from the pentacene/SiO2 and pentacene/metal interfaces. More importantly, the origin of the threshold voltage difference between ML and thick FETs is addressed through a model in which the effective charge transport layer is transitioned from the pentacene layer interfacing with the SiO2 gate dielectric to the upper layers with pentacene thickness increasing evidenced by pentacene coverage dependent threshold voltage measurements.