The ionotropic gelation technique was chosen to produce vitamin D3-loaded microparticles starting from oil-in-water (O/W) Pickering emulsion stabilized by flaxseed flour: the hydrophobic phase was a solution of vitamin D3 in a blend of vegetable oils (ω6:ω3, 4:1) composed of extra virgin olive oil (90%) and hemp oil (10%); the hydrophilic phase was a sodium alginate aqueous solution. The most adequate emulsion was selected carrying out a preliminary study on five placebo formulations which differed in the qualitative and quantitative polymeric composition (concentration and type of alginate selected). Vitamin D3-loaded microparticles in the dried state had a particle size of about 1 mm, 6% of residual water content and excellent flowability thanks to their rounded shape and smooth surface. The polymeric structure of microparticles demonstrated to preserve the vegetable oil blend from oxidation and the integrity of vitamin D3, confirming this product as an innovative ingredient for pharmaceutical and food/nutraceutical purposes.