We report on fully quantum electronic-nuclear dynamics following sudden ionization from the neutral in the three lowest electronic states of the CH4 + and CD4 + cations. There is a strong Jahn–Teller effect in the Franck–Condon region, and we employ two nuclear degrees of freedom that span the internal coordinates involved in the Jahn–Teller coupling. The initial state results from tunneling ionization by a strong IR field which coherently pumps the three lowest states of the cation, D0, D1, and D2. The quantum dynamical simulations show that a strong isotope effect occurs when the ionization significantly accesses the D2 state of the cation in the Franck–Condon region. The computed isotope effect is larger than expected on the basis of the effective mass ratio. The strong effect is due to fast oscillations of the electronic coherences between the D2 and the D1 and D0 electronic states and their modulation by the nonadiabatic couplings before a significant onset of nuclear motion. The magnitude of the effect is similar to the one that we previously reported for a sudden photoionization process. A strong isotope effect has been observed in high harmonic spectroscopy studies of the very short time dynamics Jahn–Teller structural rearrangement of the methane cation upon sudden ionization.