Organic field-effect transistors including a functional bio-recognition interlayer, sandwiched between the dielectric and the organic semiconductor layers, have been recently proposed as ultrasensitive label-free biosensors capable to detect target molecule in the low pM concentration range. The morphology and the structure of the stacked bilayer formed by the protein bio-interlayer and the overlying organic semiconductor is here investigated for different protein deposition methods. X-ray scattering techniques and scanning electron microscopy allow to gather key relevant information on the interface structure and to assess target analyte molecules capability to percolate through the semiconducting layer reaching the protein deposit lying underneath. Correlations between the structural and morphological data and the device analytical performances are established allowing to gather relevant details on the sensing mechanism and further improving sensor performances, in particular in terms of sensitivity and selectivity.