In this paper we report a novel acid-modulated strategy for peptide microarray production on biosensor interfaces. We have initially selected controlled pore glass (CPG) as support for solid phase peptide synthesis (SPPS) to implement a chemistry that can be efficiently performed at the interface of multiple FET sensors, eventually to generate label-free peptide microarrays for protein screening. Our chemistry uses temporary protection of the N-terminal amino function of each amino acid building block with a tert-butyloxycarbonyl (Boc) group that can be removed after each SPPS cycle, in combination with semi-permanent protection of the side chains of trifunctional amino acid residues. Such protection scheme, with a well-proven record of application in conventional, batchwise SPPS, has been fine tuned for optimal performance on CPG and, from there, translated to SPR chips that allow layer-by-layer monitoring of amino acid coupling. Our results validate this acid-modulated synthesis as a feasible approach for producing peptides in high yield and purity on flat glass surfaces such as those in bio-FETs.