In this article, we report on the successful implementation of nanoparticle incorporation and acid doping in tuning the properties of chitosan for proton-based ion gating of metal–oxide electric double layer transistors (EDLTs). SiO₂ nanoparticle (nano-SiO₂) incorporation was initially found to produce rougher surfaces, lower the specific capacitance and postpone the transport of protons, which deteriorated the performance of the transistors. The advantage of nano-SiO₂ incorporation lies in their ability to significantly improve the transistor's negative bias stability due to a proposed proton blocking mechanism. By applying doping of H₃PO₄, the negative effects of nano-SiO₂ incorporation were partially counterbalanced. This is because H₃PO₄ can donate more protons and assist the proton conduction via the donor/acceptor process of amphoteric acids or forming the molecular network of hydrogen bonds. Overall, this work presents a promising strategy to optimize the bio-polyelectrolyte gated EDLTs by combining nanoparticle incorporation and acid doping.