Pinch-off voltage is a key device characteristic of depletion-mode pseudomorphic high electron mobility transistors (pHEMT). Pinch-off voltage (Vp) shifts caused by manufacturing process variation were studied in this paper. Experimental results showed higher pinch-off voltage if the AlGaAs Schottky layer is oxidized or contaminated by metal. A significant increase in pinch-off voltage was observed when the Schottky layer was exposed to air for up to 2 hours after oxygen plasma treatment. Investigation also revealed an increase in pinch-off voltage in relation to staging time and environment before gate contact metal deposition. In both cases, the effective thickness of the AlGaAs Schottky layer was reduced, and pinch-off voltage was increased. Models of metal cross-contamination and a “last wafer” effect in wet clean processing were also evaluated to address pinch-off voltage variation.