Short channel organic thin film transistors in bottom-gate, bottom contact configuration use typically gold metallization for the source and drain contacts because this metal can easily be cleaned from photoresist residuals by oxygen plasma or ultraviolet-ozone and allows also surface modification by self-assembled monolayers (e.g. thiols). Alternative low-cost bottom contact metallization for high performance short-channel organic thin film transistors are scarce because of the incompatibility of the bottom contact material with the cleaning step. In this work a new process flow, involving a temporary thin aluminum protection layer, is presented. Short channel (3.4 μm) pentacene transistors with lithographical defined and thiol modified silver source/drain bottom contacts (25 nm thick, on a 2 nm titanium adhesion layer) prepared according to this process achieved a saturation mobility of 0.316 cm2/(V.s), and this at a metal cost below 1% of the standard 30 nm thick gold metallization.