We present a method for forming monodisperse semi-permeable microcapsules composed of an alginate-poly-L-lysine (PLL) membrane for the observation of encapsulated cells. These microcapsules were prepared with a monolithic three-dimensional microfluidic axisymmetric flow-focusing device by an internal gelation method using glucono-1,5-lactone in order to provide mild conditions for the cells. The microcapsules were sufficiently monodisperse and robust to be trapped in a bead-based microfluidic array system for easy observation. We also confirmed that (i) the alginate-PLL membrane is semi-permeable so that cells and microorganisms cannot pass through it but nutrients and wastes can, (ii) cells are able to move freely inside the semi-permeable microcapsules, and (iii) cells can be successfully proliferated in the microcapsules.