This work evaluated maltodextrin/alginate and β-glucan/alginate mixtures in the food industry as wall materials for the microencapsulation ofSchizochytriumsp. oil, an important source of the omega-3 fatty acid DHA (docosahexaenoic acid). Results showed that both mixtures display a shear-thinning behavior, although the viscosity is higher in β-glucan/alginate mixtures than in maltodextrin/alginate. Scanning electron microscopy was used to assess the morphology of the microcapsules, which appeared more homogeneous for maltodextrin/alginate. In addition, oil-encapsulation efficiency was higher in maltodextrin/alginate mixtures (90%) than in β-glucan/alginate mixtures (80%). Finally, evaluating the microcapsules’ stability by FTIR when exposed to high temperature (80 °C) showed that maltodextrin/alginate microcapsules were not degraded contrary to the β-glucan/alginate microcapsules. Thus, although high oil-encapsulation efficiency was obtained with both mixtures, the microcapsules’ morphology and prolonged stability suggest that maltodextrin/alginate is a suitable wall material for microencapsulation ofSchizochytriumsp. oil.