AbstractRecent advances in magnetic nanocomposites have enabled untethered micromachines with controllable shape transformations and programmable magnetic anisotropy, paving the way for a variety of biomedical applications using soft microrobots. Magnetic anisotropy is programmed by assembling the embedded magnetic nanoparticles (MNPs) in polymeric materials to overcome the shape anisotropy of a given structure. However, this approach is questionably effective in reconfigurable structures, as shape changes naturally result in rearrangement of the embedded MNPs. A naturally occurring solution to this problem is found in magnetotactic bacteria, which build chains of MNPs in a linear‐chain formation in their cells to create a permanent magnetic dipole moment. This dipole moment enables them to actively sense magnetic fields and coordinate their movement in response, a behavior called magnetotaxis. Inspired by this, self‐folding micro‐origami swimmers comprising magnetic nanocomposite bilayer structures that exhibit controllable shape transformations and programmable, shape‐independent magnetotaxis is fabricated. A study of these structures reveals that their magnetic anisotropy results from competition or cooperation between anisotropy of assembled chains of MNPs and overall shape anisotropy. Moreover, how the magnetotaxis of the reconfigurable micro‐origami swimmers depends only on the embedded permanent dipole moment, independent of the overall magnetic anisotropy, is demonstrated.