The structural transformations occurring during high‐energy mechanical milling and subsequent annealing of YBa2Cu3O7-δ samples have been studied. A high initial oxygen content favors the formation of a metastable (Y0.33Ba0.66)CuO3-x disordered cubic phase. The cubic phase decomposes into a nanocrystalline mixture of Y2BaCuO5 and an yttrium deficient amorphous phase upon further milling. The crystallization enthalpy of the amorphous phase was estimated to be approximately 72.2 kJ/mol with a corresponding activation energy of 800±80 kJ/mol. Upon heating the nanocrystalline cubic phase transforms to the high‐oxygen tetra X (O6.77) nonsuperconducting phase. Under oxygen, this last phase is stable up to 930 °C where it transforms to the tetra II low‐oxygen (O≪6.4) structure which reverts to the ortho I superconducting phase after adequate cooling. A structural model is proposed in which the formation of coherent domain boundaries and the unusually short c axis associated with the tetra X phase are related to the reordering of the Y‐Ba sublattice of the metastable cubic phase. The relative stability of the cubic and tetra X phases as a function of the initial oxygen content before milling indicates that the oxygen concentration may be higher at the domain boundaries.