This study aimed to examine the impact of naturally derived hydroxyapatite (HA) particles on the surface characteristics and corrosion behavior of polypyrrole (PPy)/polypyrrole-HA bilayer coatings. The coatings were applied onto AZ31 Mg alloy substrates using the potentiostatic electrodeposition method. Varying concentrations of HA particles (1, 3, and 5 wt%) were incorporated into the electrodeposition baths to create the top composite layers. Morphological analysis using FESEM revealed that the presence of HA particles led to PPy coatings with reduced porosity and more compact structures. EDS analysis and elemental mapping confirmed the presence of HA particles within the PPy matrix. AFM topography parameters indicated a slight increase in roughness values as the concentration of HA particles increased, with the average roughness rising from 46 nm for pure PPy coating to 53 nm for the coating with the highest HA content. Wettability results showed that the water contact angle (WCA) decreased from 56.6° for unreinforced PPy to 35.6° for the bilayer PPy/PPy-5 wt%HA coating. The corrosion behavior of the samples was investigated using potentiodynamic polarization and electrochemical impedance spectroscopy. It was observed that HA particles effectively reduced the corrosion current density (icorr), with the icorr of the optimal bilayer coating containing 3 wt% HA being 3.7 × 10−7 A cm−2, approximately two times lower than that of unreinforced PPy coating. Furthermore, the adhesion strength of the coatings was not affected by the inclusion of HA particles.