There is an increased interest in the use of the deep eutectic solvents (DESs) as electrolytic media for electrochemical synthesis of conducting polymers, which could influence their characteristics. Moreover, the polypyrrole layers represent an attractive route for pharmaceutical drug release. The paper presents several experimental results regarding the electrodeposition of polypyrrole and of polypyrrole-indomethacin coatings on nickel-chromium NiCr alloy substrates widely used in dentistry, involving DES-based electrolytes, namely eutectic mixtures of choline chloride and malonic acid. This type of electrolyte also allowed an enhanced dissolution of indomethacin as compared to aqueous ones. The electropolymerization process has been investigated by cyclic voltammetry and chronoamperometry. The obtained indomethacin containing polymeric coatings have been thoroughly characterized involving scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, contact angle measurements in simulated body fluid (SBF) and indomethacin release studies. Adherent and uniform polypyrrole-indomethacin layers have been obtained on NiCr alloy substrates. The release tests showed that the polypyrrole coatings containing indomethacin may deliver the drug molecules for longer periods of at least 17 days. The maximum released amount was around 99.6% suggesting these layers may act as an active reservoir for indomethacin. Kinetics analysis based on the Korsmeyer–Peppas model suggested the diffusion of the drug out of the polymer layer as the most probable mechanism governing the release.