The automation of liquid handling routines offers great potential for fast, reproducible and laborreduced biomaterials fabrication but also requires the development of special protocols. Competitive systems demand for a high degree in miniaturization and parallelization while maintaining flexibility regarding the experimental design. To day, there are only few possibilities for automated fabrication of biomaterials inside multi-well plates. We have previously demonstrated that streptavidin-based biomimetic platforms can be employed to study cellular behaviors on biomimetic surfaces. So far, these self-assembled materials were made by stepwise assembly of the components using manual pipetting. In this work, we introduce for the first time a fully automated and adaptable workflow to functionalize glass-bottom multi-well plates with customized biomimetic platforms deposited in single wells using a liquid handling robot. We then characterize cell response using automated image acquisition and subsequent analysis. Furthermore, the molecular surface density of the biomimetic platforms was characterized in situ using fluorescence-based image correlation spectroscopy. These measurements were in agreement with standard ex situ spectroscopic ellipsometry measurements. Thanks to automation, we could do a proof-of-concept to study the effect of heparan sulfate on the bioactivity of bone morphogenetic proteins on myoblast cells, using four different BMPs (2,4,6 and 7) in parallel, at five increasing concentrations. Using such automated self-assembly of biomimetic materials, it may be envisioned to further investigate the role of a large variety of ECM components and growth factors on cell signaling.