The effects of intermediate charmed mesons on charmonium transitions with the emission of one pion or eta are studied systematically. Based on a non-relativistic effective field theory we show that charmed meson loops are enhanced compared to the corresponding tree-level contributions for transitions between two S-wave charmonia as well as for transitions between two P-wave charmonia. On the contrary, for the transitions between one S-wave and one P-wave charmonium state, the loops need to be analyzed case by case and often appear to be suppressed. The relation to and possible implications for an effective Lagrangian approach are also discussed. This study at the same time provides a cross check for the numerical evaluations.