Computational Fluid Dynamics (CFD) simulations to predict forces from a Wind Propulsion Unit (WPU) on a ship hull are carried out to better understand the forces dependency on wind speed and angle. Three different Atmospheric Boundary Layer (ABL) stratifications, nominally unstable, neutral, and stable, are studied in a CFD environment to better understand how to reproduce these velocity profiles numerically and how much is their impact on the performance of a general ship’s hull equipped with a Flettner rotor. A series of 2D and 3D simulations with an empty domain are run to tune some numerical settings for a correct representation of the ABL. Simulations with a simplified hull and a Fletter rotor are run to purely analyse the differences between the profiles and their effects on a reproduceable geometry. The three different ABL profiles are tested for four different wind angles, producing an overview of the dependency of rotor and ship performance on wind speed profiles, wind angles and hull interaction. A clear impact of the wind profiles and the wind angle on the ship hull is visible on the rotor lift and drag coefficients, while in terms of ship performance, described by the ratio of the thrust and side force coefficients, the impact is limited