Current tissue engineering approaches for most part utilize either a scaffold-based or a scaffold-free strategies. Recently, a third strategy demonstrated a synergetic method leveraging the benefits of both approaches without their typical disadvantages. For this, spheroids are formed within highly porous microscaffolds that then act as building blocks for larger tissue constructs produced by self-assembly. The work presented here demonstrates the fabrication of a large number of such building blocks in an automated way, tested in up to 1536-well plates. We first developed a microfluidic device capable of sorting highly porous microscaffolds with a diameter of 300 µm at high flow speeds of up to 300 mm/s. A fluorescent setup was developed to single out only intact microscaffolds and deposit them one-by-one in separate wells of cell culture plates. Subsequently, the system automatically dispensed culture medium with suspended human adipose-derived stem cells into each well. Spheroids were formed within 24 hours of culture with a formation efficiency of 95%. This study reports the development of an automated microfluidic device capable of depositing single microscaffolds and the cells required to form scaffolded spheroids, thereby enabling the benefits of the third strategy of tissue engineering at scale fit for screening applications and clinical translation.