Following the methodology of Brasco (Adv Math 394:108029, 2022), we study the long-time behavior for the signed fractional porous medium equation in open bounded sets with smooth boundary. Homogeneous exterior Dirichlet boundary conditions are considered. We prove that if the initial datum has sufficiently small energy, then the solution, once suitably rescaled, converges to a nontrivial constant sign solution of a sublinear fractional Lane–Emden equation. Furthermore, we give a nonlocal sufficient energetic criterion on the initial datum, which is important to identify the exact limit profile, namely the positive solution or the negative one.