We performed transient absorption (TA) measurements on CP29 minor light-harvesting complexes that were reconstituted in vitro with either violaxanthin (Vio) or zeaxanthin (Zea) and demonstrate that the Zea-bound CP29 complexes exhibit charge-transfer (CT) quenching that has been correlated with the energy-dependent quenching (qE) in higher plants. Simulations of the difference TA kinetics reveal two-phase kinetics for intracomplex energy transfer to the CT quenching site in CP29 complexes, with a fast <500 fs component and a similar to 6 ps component. Specific chlorophyll sites within CP29 are identified as likely locations for CT quenching. We also construct a kinetic model for CT quenching during qE in an intact system that incorporates CP29 as a CT trap and show that the model is consistent with previous in vivo measurements on spinach thylakoid membranes. Finally, we compare simulations of CT quenching in thylakoids with those of the individual CP29 complexes and propose that CP29 rather than LHCII is a site of CT quenching.