The use of dexamethasone (DEX) as a mainstay drug for controlling inflammation is hampered by its unfavorable pharmacokinetics and systemic side effects. Mesoporous silica nanoparticles (MSNs) have been identified as a viable delivery strategy due to their unique features, such as tunable pore size, shape, and surface area, as well as biocompatibility, and surface function ability, and stability. In the present study, amine-functionalized MSNs with an average diameter of 88 nm, mean specific surface area of 498 m2/g, and mean pore size of 2.4 nm were fabricated and modified first with palmitoyl chloride (MSN-PALM) to improve drug loading. The impact of different degrees of MSN palmitoylation was explored on the DEX loading and particle size distribution. To avoid unfavorable interactions of MSN silanol groups with bio-membranes, as well as to improve colloidal dispersion and to sustain drug release, DEX-loaded MSN and MSN-PALM were combined with lipid bilayers containing PEG-phospholipids and then probe sonicated to obtain MSN-LC or MSN-PALM-LC, respectively. The preparations were characterized using DLS, FE-SEM, TGA, FTIR, XRD, and BET techniques, and then optimized by modifying the degree of palmitoylation, and lipid bilayer composition, and the weight ratio of phospholipids to the carrier using a full factorial design approach. Equilibrium surface adsorption of DEX was evaluated by comparing different isotherms including Langmuir, Freundlich, and Temkin. In-vitro release profiles of DEX from MSN, MSN-PALM, MSN-LC, and MSN-PALM-LC in phosphate buffer (pH = 7.4) were evaluated, and the drug release data were fitted to various kinetic models. Drug loading (%) reached to 35% (w/w) in 1:1 drug/carrier ratio in MSN-PALM13. Initial fast drug release from MSN-NH2 and MSN-PALM13 continued for 12 h, resulting in a drug release of about 61% and 47%, respectively. After lipid coating, initial fast release of DEX decreased to about 26% and 19%, respectively. The hemolysis test indicated that palmitoylation in high ratios and supported lipid coating to a greater extent improved hemocompatibility. Finally, surface engineered MSNs have shown high-capacity DEX loading, long-term release, and hemocompatibility, suggesting their potential application in chronic inflammatory diseases.