Microcapsules with controlled stability and permeability are in high demand for applications in separation and encapsulation. We have developed a biointerfacial process to fabricate strong, but flexible, porous microcapsules from bacterial cellulose at an oil-water emulsion interface. A broad range of microcapsule sizes has been successfully produced, from 100 μm to 5 cm in diameter. The three-dimensional capsule microstructure was imaged using confocal microscopy, showing a cellulose membrane thickness of around 30 μm that is highly porous, with some pores larger than 0.5 μm that are permeable to most macromolecules by free diffusion but can exclude larger structures like bacteria. The mechanical deformation of cellulose microcapsules reveals their flexibility, enabling them to pass through constrictions with a much smaller diameter than their initial size by bending and folding. Our work provides a new approach for producing soft, permeable, and biocompatible microcapsules for substance encapsulation and protection. The capsules may offer a replacement for suspended polymer beads in commercial applications and could potentially act as a framework for artificial cells.