The bacteriocin nisin has been extensively used as potential natural preservative in the food industry. However, antimicrobial activity of nisin due to its binding with food components and inactivation by enzymatic degradation is reduced when it is applied in food. Encapsulation of nisin is an efficient approach to overcome the problems related to the direct application of this antimicrobial peptide in foods. In this study, nisin was encapsulated in alginate-high methoxy pectin (HMP) microparticles, and its release studies were performed in water to determine the diffusion and the kinetic behaviour of the matrix. Results showed that the nisin content had a significant influence on encapsulation efficiency (EE), loading capacity (LC) and microparticles size. The values of EE, LC and particle mean diameter were about 47–54%, 16–21% and 57–131 μm, respectively. The nisin-loaded microparticles showed nearly spherical structure with fold on the surface, as displayed by scanning electron micrograph. Interaction between alginate and HMP was confirmed by the changes in the intensity and wave number of the stretching vibrations of the hydroxyl and carboxyl groups in alginate-HMP microparticles FTIR spectra. Furthermore, the addition of nisin resulted in a markedly increase in intensity of carboxylic peak at 1620 cm−1, indicating the presence of nisin inside of the microparticles. The in vitro nisin release from these microparticles followed a sustained release profile consistent with a Fickian diffusion mechanism.