We apply a 3D adaptive refinement procedure using meshless generalized finite difference method for solving elliptic partial differential equations. This adaptive refinement, based on an octree structure, allows adding nodes in a regular way in order to obtain smooth transitions with different nodal densities in the model. For this purpose, we define an error indicator as stop condition of the refinement, a criterion for choosing nodes with the highest errors, and a limit for the number of nodes to be added in each adaptive stage. This kind of equations often appears in engineering problems such as simulation of heat conduction, electrical potential, seepage through porous media, or irrotational flow of fluids. The numerical results show the high accuracy obtained.