Peptides are excellent building blocks to form precise nanostructures by self-assembly. They can selfassemble into fibril nanostructures, thus recreating some of the architectural features of the natural extracellular matrix. Here, we used a microfluidic approach to drive the self-assembly of peptides of opposite charge into capsular structures for cell encapsulation. The obtained capsules presented a core shell structure made of a network of nanofibers and their properties can be tuned by varying the concentration of each peptide. Capsules were found to be stable in aqueous solutions and their permeability dependent on the capsule composition. Human dermal fibroblasts were encapsulated and remained viable within the capsules and their morphology was shown to be influenced by the matrix density. Additionally, these capsules also supported the co-culture of fibroblasts and keratinocytes. We expect that the developed peptide-based microcapsules can serve as miniaturized environments for cell culture and as biomimetic platforms for in vitro drug screening.