<p>This study explores the influence of the anionic moiety of imidazolium-based ionic liquids (ILs) on the thermoelectric properties of polypyrrole (PPy). The selected ionic liquids have gained significant attention due to their interesting electrical and thermal properties, which can enhance the thermoelectric performance of polymer-based materials. In this work, a series of polypyrrole-based composite materials were processed with different imidazolium ILs, varying the nature of the counter anions to investigate their effect on the electrical conductivity, Seebeck coefficient, and thermal conductivity of the polymer. Through a combination of physicochemical and thermoelectric characterization, including Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and thermoelectric measurements, the effect of the ionic liquid on the physicochemical and thermoelectric properties of polypyrrole was investigated. The results demonstrated that the anionic structure plays a key role in enhancing the thermoelectric properties of PPy. In fact, the incorporation of 1-ethyl-3-methylimidazolium tetrachloroferrate(III) (EMImFeCl₄) led to a significant improvement in the Seebeck coefficient (<i>S</i> = 384.615&#xa0;µV·K⁻¹), with PPy-EMImFeCl₄ showing the most notable increase in terms of figure of merit (<i>ZT</i> = 5.109 × 10⁻³), which was approximately 250 times that of the neat polypyrrole. This effect is also attributed to the ability of EMImFeCl₄ to reduce the thermal conductivity (κ = 0.069&#xa0;W·m⁻¹·K⁻¹).</p> Graphical Abstract <p></p>