We investigated the in situ growth of YBa2Cu3O7−δ superconducting thin films by a sequential ion beam sputtering technique, studying the relations among deposition parameters, structural and superconducting properties. The films were deposited following the stacking sequence of YBa2Cu3O7−δ, with individual layer thicknesses nominally equal to one monolayer. O2 was supplied during deposition. Predominantly c-axis oriented films were grown on (100) SrTiO3, (100) MgO, and oxidized Si (SiO2/Si) substrates. The microstructure and film-substrate orientation relations were studied by transmission electron microscopy. X-ray studies showed the presence of homogeneous and inhomogeneous strains along the c-direction that persisted after low temperature oxygen anneals. Resistivity measurements showed correlations between the superconducting transition characteristics and the lattice distortions along the c-direction. The effect of deposition parameters on the lattice distortions was investigated, finding that the c-axis lattice parameter was larger in films grown at lower temperatures. This was interpreted in terms of the thermally activated dissociation of O2 at the film surface during growth. We assumed that the c-axis lattice expansion was due to kinetic limitations to the incorporation of oxygen into the film during growth. This led to a consistent description of the results obtained in this work and the O2 pressure dependence of the c-axis lattice expansion reported for other in situ techniques. Studies were performed on films grown by this technique as well as on films grown in situ by magnetron sputtering in an attempt to elucidate the nature of the defect structure causing the c-axis lattice distortions.