We construct the gauge invariant free action for cosmological perturbations for the nonminimally coupled inflaton field in the Jordan frame. For this the phase space formalism is used, which keeps track of all the dynamical and constraint fields. We perform explicit conformal transformations to demonstrate the physical equivalence between the Jordan and Einstein frames at the level of quadratic perturbations. We show how to generalize the formalism to the case of a more complicated scalar sector with an internal symmetry, such as Higgs inflation. This work represents a first step in developing gauge invariant perturbation theory for nonminimally coupled inflationary models.