Synchronization occurs widely in the natural and technological worlds, from the rhythm of applause and neuron firing to the quantum mechanics of coupled Josephson junctions, but has not been used to produce new spatial structures. Our understanding of self-assembly has evolved independently in the fields of chemistry and materials, and with a few notable exceptions has focused on equilibrium rather than dynamical systems. Here we combine these two phenomena to create synchronization-selected microtubes of Janus colloids, micron-sized spherical particles with different surface chemistry on their opposing hemispheres, which we study using imaging and computer simulation. A thin nickel film coats one hemisphere of each silica particle to generate a discoid magnetic symmetry, such that in a precessing magnetic field its dynamics retain crucial phase freedom. Synchronizing their motion, these Janus spheres self-organize into micrometre-scale tubes in which the constituent particles rotate and oscillate continuously. In addition, the microtube must be tidally locked to the particles, that is, the particles must maintain their orientation within the rotating microtube. This requirement leads to a synchronization-induced structural transition that offers various applications based on the potential to form, disintegrate and fine-tune self-assembled in-motion structures in situ. Furthermore, it offers a generalizable method of controlling structure using dynamic synchronization criteria rather than static energy minimization, and of designing new field-driven microscale devices in which components do not slavishly follow the external field.