We demonstrate a simple and fast method for self-assembly-driven micropatterning of protein functionalized magnetic beads on glass. We use positively charged aminosilane micro-patterns as template for selective immobilization of streptavidin-coated beads by electrostatic interactions. We show that addition of a non-ionic surfactant to the bead solution increases the selectivity of the micropatterning process. Streptavidin-coated magnetic beads (1 micron and 2.8 microns in size) are immobilized, with high reproducibility and in a very short processing time (~ 30 minutes), in the form of stripes and dots, both on bare substrates and in situ in microfluidic channels. The arrangement and the number of immobilized beads can be controlled by tuning the aminosilane template size.