Surface modification of titanium alloys constitutes one of the key development directions of modern biomaterials used in orthopedic and dental implantology. This study presents the results of investigations into the influence of parameters of a two-step surface modification of the Ti-13Zr-13Nb alloy, including micro-arc oxidation (MAO) and electrophoretic deposition (EPD), on the properties of the obtained surface layers. The MAO process was carried out for 5 and 10 minutes in an electrolyte containing calcium and phosphorus compounds. Subsequently, a nanohydroxyapatite coating with the addition of silver nanoparticles was deposited on the modified surfaces using the EPD method. The obtained samples were subjected to comprehensive characterization, including Vickers microhardness measurements, evaluation of coating thickness and uniformity, analysis of surface morphology and chemical composition (SEM/EDS), wettability and surface free energy measurements, coating adhesion tests, and cell studies. The results demonstrated a significant increase in microhardness and surface hydrophilicity after MAO–EPD modification compared to the reference material. The obtained Ca/P ratio was close to that of natural bone, indicating the bioactive potential of the produced layers. Indirect cytotoxicity testing revealed that EPD-modified surfaces and MAO (10 min) combined with EPD were noncytotoxic, maintaining viability above 90. In contrast, MAO (5 min) + EPD extracts significantly reduced cell viability to approximately 65–70%. The MAO 5 min + EPD variant achieved other favorable properties, as it exhibited good uniformity, high microhardness, and acceptable coating adhesion. The results confirm the validity of applying the two-step surface modification of the Ti-13Zr-13Nb alloy in the design of bioactive implant surfaces.