Integrated lab-on-chip (LOC) microsystems dedicated to proteomic analysis require specific pretreatment steps such as protein trypsic digestion, concentration, desalting or separation of biological samples. These steps can be achieved thanks to porous monolithic polymers. This paper deals with the integration of such a polymer into SU-8 microchannels by using a multi-material technology (SU-8, Pyrex and silicon). A solution for the fabrication of complete polymer microchannels which are high pressure- and solvents-resistant is proposed. This technique uses the negative photoresist SU-8 which is compatible with the protein analysis performed here. Our process requires a novel technological step using a silane coupling agent. This modification of the SU-8/Pyrex interface leads to the fabrication of a 100 νm × 160 νm section microchannel (length of 3 cm), closed with a Pyrex lid by SU-8 bonding resistant to 80 bar. An improvement of the SU-8/monolithic structure is also demonstrated thanks to a specific treatment of the polymer enabling good anchoring of the monolith in the microchannels, and the pressure-resistance tests were also achieved with the monolithic structure integrated in the microchannels. A digestion step of a protein sample of benzoylarginine ethyl ester in a SU-8 microchannel was achieved after the functionalization of a monolith anchored in the microchannel. Analysis by UV/VIS spectroscopy of this in situ digestion has been reported.