The insufficiency of vitamin D, resulting from inadequate exposure to sunlight and/or insufficient dietary intake, remains a major public health concern on a global scale. In this study, vitamin D2 and D3 were microencapsulated using sporopollenin exine microcapsules extracted from Cedrus libani pollens. After loading vitamin D into the microcapsules, they were coated with chitosan, an edible, biocompatible, and mucoadhesive polysaccharide, and alginate (a food additive agent coded E401). Exine microcapsules were extracted by microwave irradiation-assisted chemical method, and structural and morphological examination of exine structures was performed by FT-IR, TGA, SEM, and SEM-EDX analyses. After loading vitamin D into microcapsules in an ethanol medium, the loaded microcapsules were immobilised into the alginate matrix in a calcium chloride solution. D2 and D3 were loaded into 100 mg of sporopollenin exine microcapsules, resulting in loading efficiencies of 31.5 mg and 16.0 mg, respectively. The vitamin D release performance of the microcapsules was examined depending on time and temperature after they were coated with a thin chitosan layer. The release of the highest amount of vitamin D2 and D3 occurred at a temperature of 37°C. Encapsulating vitamin D molecules in chitosan and alginate creates a barrier against degrading environmental conditions, which helps prevent the loss of vitamin D biological activity. This can improve vitamin D dietary supplements' storage, preservation, and marketing requirements.