Porous titanium alloy Ti6Al4V scaffolds manufactured via electron beam melting (EBM®) reveal broad prospects for applications in bone tissue engineering. However, local inflammation and even implant failure may occur while placing an implant into the body. Thus, the application of drug carriers to the surface of a metallic implant can provide treatment at the inflammation site. In this study, we propose to use polyelectrolyte (PE) microcapsules formed by layer-by-layer (LbL) synthesis loaded with both porous calcium carbonate (CaCO3) microparticles and the anti-inflammatory drug dexamethasone (DEX) to functionalize implant surfaces and achieve controlled drug release. Scanning electron microscopy indicated that the CaCO3 microparticles coated with PE bilayers loaded with DEX had a spherical shape with a diameter of 2.3 ± 0.2 μm and that the entire scaffold surface was evenly coated with the microcapsules. UV spectroscopy showed that LbL synthesis allows the manufacturing of microcapsules with 40% DEX. According to high performance liquid chromatography (HPLC) analysis, 80% of the drug was released within 24 h from the capsules consisting of three bilayers of polystyrene sulfonate (PSS) and poly(allylamine)hydrochloride (PAH). The prepared scaffolds functionalized with CaCO3 microparticles loaded with DEX and coated with PE bilayers showed hydrophilic surface properties with a water contact angle below 5°. Mouse embryonic fibroblast cells were seeded on Ti6Al4V scaffolds with and without LbL surface modification. The surface modification with LbL PE microcapsules with CaCO3 core affected cell morphology in vitro. The results confirmed that DEX had no toxic effect and did not prevent cell adhesion and spreading, thus no cytotoxic effect was observed, which will be further studied in vivo.