In this paper, a three-dimensional integrated numerical model for a small-scale case of wave-induced oscillatory soil response around a semi-buried pipeline (PORO-WSSI-PIPE 3D) is proposed. In this model, we combine the Reynolds-averaged Navier–Stokes (RANS) equations for the 3D wave motions and the Biot’s consolidation equations for a porous elastic seabed foundation through pressure continuity at common boundaries, with pipeline being an elastic and impermeable medium. The computational results are validated through comparison with previous analytical solutions and laboratory wave flume tests, obtaining good agreement. Following validation, the numerical model is applied to simulate wave-seabed-pipeline interaction with different obliquities between pipeline and incident wave, varying from 30 deg to 90 deg. Snapshots of wave-seabed-pipeline interaction, as well as dynamic pore pressure distributions at typical locations in the vicinity of a semi-buried pipeline, are obtained and analyzed. The three-dimensional consolidation process of seabed under gravitational forces including the body forces of a pipeline is also discussed.