Hair regenerative medicine is a promising approach for hair loss, during which autologous follicular stem cells are transplanted into regions of hair loss to regenerate hairs. Because cells transplanted as a single cell suspension scarcely generate hairs, the engineering of three-dimensional (3D) tissues before transplantation has been explored to improve this process. Here, we propose an approach to fabricate collagen-enriched cell aggregates, named hair beads (HBs), through the spontaneous constriction of cell-encapsulated collagen drops. Mouse embryonic mesenchymal cells or human dermal papilla cells were encapsulated in 2-μl collagen microgels, which were concentrated >10-fold in volume during 3 days of culture. Interestingly, HB constriction was attributed to attraction forces driven by myosin II and involved the upregulation of follicular genes. Single HBs with epithelial cells seeded in U-shaped microwells formed dumbbell-like structures comprising respective aggregates (named bead-based hair follicle germs, bbHFGs), during 3 days of culture. bbHFGs efficiently generated hair follicles upon intracutaneous transplantation into the backs of nude mice. Using an automated spotter, this approach was scalable to prepare a large number of bbHFGs, which is important for clinical applications. Therefore, this could represent a robust and practical approach for the preparation of germ-like tissues for hair regenerative medicine.