Regenerative medicine has increasingly made use of adult stem cells in the last years (1, 2). Micro-engineering a biomimetic three dimensional structure provides a realistic approach for stem cell niche studies, and further translational applications. A promising approach for engineering artificial stem cell niches is provided by high-throughput microfluidic technologies. In this work, a droplet-based microfluidic-assisted encapsulation device for the generation of multi-layered cellular structures on demand using alginate and Puramatrix is presented. This novel technology is based on gravity-driven flows, passive mixing principle and a gelation system where the use of a double laminar oil flow where only one contains the cross-linking agent allows both the uniform gelation of the inner core and the continuous generation of a stream of cross-linked hydrogel beads. The soft consecutive coating of the inner core with a second and a third layer without exposing the encapsulated cells to external forces that might reduce their viability represents a promising technology towards 3D stem cell encapsulation. Furthermore, we demonstrate the suitability of the presented technology for encapsulation of stem cells by using human Mesenchymal Stem cells (hMScs) and human Hematopoietic stem cells (hHScs). Preliminary results demonstrate a niche model capable of mid-term culture of primitive hHScs in a microfluidic environment. Therefore, the presented method could apply for the artificial reconstruction of the stem cell niche components as an efficient approach to study stem cell behaviour in vitro under controlled conditions, opening a wide field of potential applications within uTAS for 3D cell culture and tissue engineering applications.