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Aqueous nanoparticle dispersions represent an actual eco-friendly strategy for the organic photovoltaic technology. Nevertheless, residual surfactant, necessary for dispersion stabilization, is a concern for the electronic properties of the layers deposited from aqueous nanoparticle dispersions. Herein, we show the superior effectiveness of the soaking with acidic ethanol, compared with neutral alcohol, commonly applied to reduce the contents of residual surfactant in nanoparticle layers. Two aqueous nanoparticle dispersions are considered, based on a low energy-gap conjugated polymer and prepared with different starting concentrations of hexadecyl trimethyl ammonium bromide as surfactant. A significant reduction of the thickness of spin-coated nanoparticle layers is observed upon soaking with acidic ethanol, without alterations of the absorption spectrum. This indicates a much more effective post-deposition removal of residual surfactant compared with a soaking with neutral alcohol, which does not lead to a thickness variation. The behaviour of organic solar cells based on nanoparticle layers soaked with ethanol with different acidic levels is also investigated and discussed.