Regenerative medicine requires the use of heterogeneous scaffolds when the tissue that needs to be repaired presents a gradient in its properties and cannot be replaced by a homogeneous graft. Then, an intimate contact between the different layers is critical to guarantee the optimal performance of the construct. This work presents a procedure that allows the immobilization of collagen-based hydrogels by self-assembly onto any desired substrate, by means of a pentafluorophenyl methacrylate (PFM) coating obtained by plasma enhanced chemical vapor deposition and a collagen monolayer. The latter is attached onto the PFM-coated substrate thanks to its high reactivity towards amines and it will act as anchoring point for the subsequent collagen fibrillation and hydrogel formation. The interaction between collagen and PFM-coated substrates has been evaluated using the quartz crystal microbalance with dissipation (QCM-D) technique. In addition, QCM-D has been used to design and monitor the collagen fibril formation process. A correlation between QCM-D data and optical microscopy has been established, and fibril formation has been confirmed by atomic force microscopy (AFM).