In this paper we study the ductile breakup of tracer aggregates in an incompressible, homogeneous, and isotropic three-dimensional turbulent flow. The flow dynamics is studied by means of a direct numerical simulation, whereas the Lagrangian velocities and stress statistics along trajectories are obtained by particle tracking. We investigate the breakup dynamics under the hypothesis that aggregates are able to deform and accumulate energy. Within this framework, breakup occurs when the energy transferred to the aggregate by the flow exceeds a critical value. We contrast our predictions for ductile breakup with those obtained for brittle breakup. We observe that turbulence intermittency is crucial for the breakup of brittle aggregates, while it becomes less relevant for ductile aggregates. In the limit of highly ductile aggregates the breakup rate is dictated by the mean properties of the flow. We propose a simple model to capture this behaviour.