In the context of Effective Field Theory, the Hilbert space of states increases in an expanding universe. Hence, the time evolution cannot be unitary. The formation of structure is usually studied using effective field theory techniques. We study the constraints on effective field theory analyses of early universe models which come from demanding that the factor of the space of states corresponding to length scales where the primordial fluctuations are manifest does not suffer from the unitarity problem. For bouncing and emergent cosmologies, no constraints arise provided that the energy scale of the bounce or emergent phases is smaller than the ultraviolet (UV) cutoff scale. On the other hand, in the case of the inflationary scenario, non-trivial upper bounds on the energy scale of inflation arise.