A scheme for the silicon microfabrication of lab-on-a-chip systems with mixing based on dynamic plugs of magnetic beads is presented. The systems consist of a microfluidic channel integrated with a number of soft magnetic elements by the sides of the channel. The elements are magnetized by a homogeneous external ac magnetic field. The systems are scalable with respect to the number of magnetic bead plugs and number of parallel channels, and thus they have high potential for use in biological separation using functionalized magnetic beads. The mixing efficiency is characterized for two different geometries of the soft magnetic structures and found to be highly sensitive to the geometry and position of the structures.