DLR’s three-dimensional inverse design method for transonic wing geometries enables the design of increasingly powerful and efficient wings. After specifying a target pressure distribution, a corresponding geometry can be found automatically. By using an integro-differential formulation of the transonic small perturbation potential equation, geometry modifications can be calculated from the difference between target and actual geometry pressure distribution. Due to the strong three-dimensional character of the flow in the area of the transition from the wing to the fuselage of the aircraft, it can be assumed that geometry modifications in the spanwise direction can also lead to the desired target pressure distribution. The present work contains the implementation of a geometry modification in spanwise direction, as well as its validation on a constructed example. This is followed by a comparison of the original method with the newly implemented method for the ECOWING configuration. The comparison reveals an advantage of the newly implemented methods in the area of the wing-fuselage intersection.