The family of generalized logarithmic spirals including a control parameter is extended to the three-dimensional case. The in-plane motion is decoupled from the out-of-plane motion in such a way that the integrals of motion found in the planar problem are still preserved in the three-dimensional case. Designing a low-thrust orbit transfer decomposes in two stages: first, orbits are projected on a reference plane and the planar transfer is solved with a generalized logarithmic spiral. Second, the out-of-plane component of the motion is included in order to target the final orbit. The projection of the three-dimensional transfer orbit on the reference plane is a generalized logarithmic spiral. Arbitrary shape-based laws for the 3D motion can be considered. This paper explores a polynomial and a Fourier series shaping method, together with a polynomial steering law. A fictitious low-thrust sample return mission to Ceres is designed to show the versatility of the method.