Recently, hollow protein microcapsules have been made simply by heating the microphase separated soy glycinin microdomains. However, the properties (e.g., mechanical properties and permeability) that relate to the application of these microcapsules are unknown. In this study, the permeability of the soy glycinin microcapsules was investigated by confocal laser scanning microscopy (CLSM), as influenced by ionic strength and pH using fluorescein isothiocyanate-dextran (FITC-dextran). The glycinin microcapsules kept the integrity between pH 1 and 11.5, swelled when pH was below 3 or above pH 11, dissociated at pH above 11.5 and deswelled slightly at pH 1. When the pH increased above 11, the permeability of the microcapsule significantly increased. Remarkably, when the pH was below the isoelectric point of glycinin (approximate to pH 5), FITC-dextran spontaneously accumulated inside the microcapsule with a significantly higher concentration than that in bulk solution, as evidenced by the strong intensity increase of fluorescence. This unique feature significantly increased the loading amount of FITC-dextran. The permeability of microcapsules was also increased by adding salt but less significant than by adjusting pH. The surface of the microcapsules became coarser when the permeability increased, which was revealed by scanning electron microscopy. These results show that soy glycinin has a great potential to be used as a wall material to fabricate hollow microcapsules that could find applications in biomedicine and food industry.