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Abstract Elastic filaments driven out of equilibrium display complex phenomena that involve periodic changes in their shape. Here, the periodic deformation dynamics of semiflexible colloidal chains in an eccentric magnetic field are presented. This field changes both its magnitude and direction with time, leading to novel nonequilibrium chain structures. Deformation into S-, Z-, and 4-mode shapes arises via the propagation and growth of bending waves. Transitions between these morphologies are governed by an interplay among magnetic, viscous, and elastic forces. Furthermore, the periodic behavior leading to these structures is described by four distinct stages of motion that include rotation, arrest, bending, and stretching of the chain. These stages correspond to specific intervals of the eccentric field’s period. A scaling analysis that considers the relative ratio of viscous to magnetic torques via a critical frequency illustrates how to maximize the bending energy. These results provide new insights into controlling colloidal assemblies by applying complex magnetic fields.