We report a systematic study of the interplay between oxygen nonstoichiometry, crystal structure, and magnetic/electrotransport properties in Sr1−xNdxCoO3−δ (x = 0.1, 0.2, 0.3). High-resolution neutron powder diffraction combined with synchrotron x-ray powder diffraction reveals that increasing the oxygen content induces a structural transition from a layered I4/mmm (2ap × 2ap × 4ap) to an oxygen-deficient orthorhombic Pmmm (ap × ap × 2ap) phases with preferential oxygen-vacancy occupation. This transition is accompanied by a crossover from G-type antiferromagnetic with a weak ferromagnetic component to a ferromagnetic state, and a drastic decay in resistivity. The evolution of the magnetic and transport properties is discussed in terms of changes in the Co spin state, enhanced Co 3d –O 2p orbital overlap upon oxygen uptake, and a magnetically inhomogeneous ferromagnetic state associated with residual oxygen vacancies and mixed Co3+/Co4+ valence. Our findings experimentally confirm that the stabilization of the layered “314” structure is driven by the presence and ordering of oxygen vacancies rather than A-site cation ordering, whereas the oxygen-deficient oxidized compounds represent an intermediate orthorhombic state preceding fully stoichiometric phases.