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.