Structural transformations of superparamagnetic colloids confined within self-assembled microtubes are studied by systematically varying tube-colloid size ratios and external magnetic field directions. A magnetic field parallel to microtubes may stretch non-linear chains like zigzag chains into linear chains. Non-parallel fields induce new structures including repulsive chains of single colloids, kinked chains and repulsive dimers, which are not observed for unconfined magnetic colloids in the bulk. The formed colloidal structures are confirmed via model calculations which account for tube-colloid size ratio effects and their reconfigurability with the field direction. Furthermore, structures are formed that allow controllable switching between a helical and a non-helical state. All observed field-induced transformations in microtubes are reversible provided the microtubes are not completely filled with colloids. In addition, we demonstrate magnetic field-responsive 2D crystallization by extending control over colloidal configurations in single microtubes to multiple well-aligned microtubes.