The aim of the study was to investigate the potential of using β-glucan as wall material to microencapsulate the elderberry extract. Firstly, the extract was obtained by the water-acetone extraction method to extract mainly anthocyanins from ground dried fruits. The extract was mixed with wall materials: maltodextrin-β-glucan mixture and the control sample as a widely used combination of maltodextrin and arabic gum (92.5:7.5). In the examined samples the content of β-glucan was 0.5, 1, 2 and 3%. Properties of encapsulated extracts of final powders were measured using particle size and morphology, encapsulation efficiency, color measurement, total anthocyanin and ascorbic acid content (TAC and TAAC) methods. Our results indicated that the β-glucan wall material samples had higher process quality compared to control samples. Addition of β-glucan insignificantly decreases encapsulation efficiency. Among powders with β-glucan content, the powder with 1% β-glucan content was characterized by the smallest (24 μm) particle size. The sample with 2% β-glucan content had the highest water solubility and polydispersity index. Due to the encapsulation efficiency, moisture content, and water solubility index, the optimum condition of microencapsulation process for elderberry extract was for samples with 0.5% β-glucan as wall material content. To conclude, due to high molecular weight of β-glucan the higher than 0.5% ratio of β-glucan is not recommended for spray-drying method. However, small quantity of health-beneficial β-glucan could act as potential encapsulation agent in clean label products to replace Arabic gum.