This work describes a new route for patterning organic monolayers on oxide-free silicon by microcontact printing (µCP) on a preformed, reactive, acid-fluoride-terminated monolayer. This indirect printing approach is fast and easily preserves the oxide-free and well-defined monolayer–silicon interface, which is the most important property for potential applications in biosensing and molecular electronics. Water-contact-angle measurements, ellipsometry, attenuated total reflection infrared spectroscopy, and X-ray photoelectron spectroscopy (XPS) demonstrate the formation of the initial acid-fluoride-terminated monolayers without upside-down attachment. Subsequent printing for twenty seconds with an N-hexadecylamine-inked poly(dimethylsiloxane) stamp results in well-defined 5-µm N-hexadecylamide dots, as evidenced by atomic force microscopy and scanning electron microscopy. Printing with a flat stamp allows investigation of the efficiency of amide formation by µCP and water-contact-angle measurements, ellipsometry, and XPS reveal the quantitative conversion of the acid fluoride groups to the corresponding amide within twenty seconds. The absence of silicon oxide, even after immersion in water for 16 h, demonstrates that the oxide-free monolayer–silicon interface is easily preserved by this patterning route. Finally, it is shown by fluorescence microscopy that complex biomolecules, like functionalized oligo-DNA, can also be immobilized on the oxide-free silicon surface via µCP.