Alginate microparticles were prepared using an air atomization method and varying formulation and processing conditions. Thereafter, the size and surface morphology of alginate microparticles were characterized. The trapping efficiencies of the ketoconazole, acetaminophen, vitamin C, and Bifidobacteria bifidum as model core materials were then determined. The air atomization process produced free-flowing and small-size microparticles after the freeze-drying process. The size distribution and surface morphology varied depending on the concentration of wall-forming materials and processing conditions. Generally, the geometric mean size increased as the concentration of alginate and poly-1-lysine and the delivery rate increased, but the air pressure decreased. Most of all, the ratio of delivery rate of alginate solution and air pressure could affect the size and surface morphology of alginate microparticles. However, the geometric mean size of alginate poly-1-lysine microparticles reproducibly ranged from about 80 to 130 microm. The microparticles were irregularly spherical or elliptical. The trapping efficiencies of ketoconazole, acetaminophen, vitamin C, and bifidobacteria were determined to be 71.5%, 60.1%, 1.6%, and 31%, respectively, when alginate concentration (1.5%), poly-1-lysine concentration (0.02%), air pressure (0.75 bar), delivery rate (8 ml/min), and spraying distance (45 cm) were applied. The current microencapsulation process using the air atomization method provides an alternative to entrapping small molecules and macromolecules without using harmful organic solvents. In addition, the small-size and free-flowing alginate microparticles containing active substances can be used as an intermediate in pharmaceutical applications.